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Pathway Tools Release Note History
Pathway Tools Release Note History
This document summarizes the release history of the Pathway Tools software.
Release Notes for Pathway Tools Software Version 28.0
Released on April 9, 2024.
Navigator -- Web
- New Genome Browser: We have made several improvements to the new genome browser, called Genome Explorer.
Several problems with the comparative genome browser have been fixed and a scroll bar has been added for long
comparisons. We have also added a tracks capability whereby large-scale datasets can be displayed against the
genome. Tracks mode can be entered by starting the genome browser and then clicking the Tracks button.
Then in the resulting pop-up window, browse to a GFF file containing the tracks data. An example file can be
downloaded from this URL: http://www.ai.sri.com/pkarp/pubs/genome-explorer-tracks.gff. The dataset is described
at the start of the file.
- New tabbed pages: BioCyc web pages for reactions, pathways, and protein complexes now have tabbed
sections similar to the tabs already present in gene and metabolite pages.
- New ontology browser: A new improved ontology browser widget is available in the Ontology tabs
for BioCyc web pages. For example, navigate to this pathway and then click the Ontology tab to see the new browser:
https://ecocyc.org/pathway?orgid=ECOLI&id=TRPSYN-PWY.
Release Notes for Pathway Tools Software Version 27.5
Released on December 18, 2023.
Status of Mac M1 Port: This is the first regular release of Pathway Tools on the M1. The M1 version is fully functional.
Navigator -- Web
- New Genome Browser:
We have re-implemented the Genome Browser in JavaScript. The new version looks much like the old version,
but it is much faster -- it zooms and pans in real time (zoom with your mouse wheel or trackpad), which is a major improvement to the user experience.
And the new version has a sequence-selection capability, both for nucleotide and amino-acid sequences.
Invoke this tool using Tools → Genome → Genome Browser, and click the Quick Help button for more information.
The old genome browser is available in the same menu.
New Genome Browser examples:
- BLAST Search Enhancements: We have made multiple improvements to the BLAST search results page.
We have also modified BLAST searches so that the user can now perform a BLAST search against a set of
BioCyc organisms specified in a SmartTable (such as against a representative set of cyanobacteria).
- Sequence Pattern Search Enhancements:
We have modified sequence pattern searches so that the user can now perform a pattern search against a set of
BioCyc organisms specified in a SmartTable.
- Multi-Omics Cellular Overview:
The multi-omics painting capabilities of the Cellular Overview (metabolic map diagram) has been expanded
so that the diagram can be painted with up to four omics datasets simultaneously. Data can be painted
onto node color and size, and onto edge color and size. For example, the user could display a transcriptomics
dataset, a proteomics dataset, and two metabolomics datasets simultaneously. To run this tool, first
display the Cellular Overview with the command Tools → Metabolism → Cellular Overview; then run
the command Upload Multi-Omics Data from File in the right-sidebar menu.
- Improvements to Omics Dashboard: The Omics Dashboard has
been extended to support multi-omics datasets with either two or
three component datatypes, for example, transcriptomics,
metabolomics and proteomics data. The aggregated data for each
subsystem from all component datasets is combined into a single plot
(with dual Y-axes), so that all types of data for a subsystem can be
viewed side-by-side. Other significant extensions to the Omics
Dashboard include a new data filtering module with multiple filter
options, and the ability to customize the colors used for each data
column.
- Accessibility Improvements: We have made many improvements to the accessibility of the Navigator for disabled persons.
Release Notes for Pathway Tools Software Version 27.0
Released on April 12, 2023.
Status of Mac M1 Port: We have made great progress with the Mac M1 port of Pathway Tools, but it is still not complete.
We hope it will be available as a special release in the next few months. Thank you for your patience.
Navigator -- Web
- Comparative Genome Dashboard: This new tool enables visual comparisons of the complete
cellular machineries of multiple BioCyc organisms. It provides both broad comparisons of
many cellular subsystems as well as the ability to drill down through multiple levels of
detail to examine the presence and absence of specific genes and pathways.
Invoke this tool as Tools → Analysis → Comparative Genome Dashboard, and click the Help button for more information.
[Example]
- Omics Data Table Viewer: This new tool provides a tabular view of transcriptomics and
metabolomics datasets to complement the other omics data tools in BioCyc. Clicking on columns
in the table enables sorting of the data by multiple criteria.
Invoke this tool from the right-sidebar menu of the Cellular Overview when this diagram is painted with omics data.
Several improvements have been made to this tool beyond the previous release including
a reorganization of columns, and new Help text.
PathoLogic
- Operon predictor upgraded: Additional improvements were made to the
operon predictor that yielded small improvements to its accuracy.
New prediction features added for predicting whether adjacent genes are within the same operon
include GC content, codon-usage similarity, and same product type (protein/RNA).
The regression model was updated based on experimental operon data from EcoCyc version 27.0.
Release Notes for Pathway Tools Software Version 26.5
Released on December 14, 2022.
Navigator -- Web
- New pathway search tool: (Tools → Search → Search Pathways) enables
searching for pathways based on a set of metabolites and gene names entered by the
user. The result pathways are ranked by the number of matches.
- Sequence pattern search tool: This tool (Tools → Search → Sequence Pattern Search)
now provides expanded search options. In addition to searching the entire genome or proteome of a given organism,
the tool can search all proteins within a provided SmartTable, and can search the entire proteomes of
a set of organisms provided in an organism SmartTable.
- When painting omics data onto the Cellular Overview (metabolic network)
tool, a new Data Table Viewer enables the user to send the omics data to a tabular
viewer tool, such as to enable sorting of the omics data by omics data value. The entire omics dataset can be sent to this table
viewer, or the user can send all data from a given pathway category (e.g., Amino Acid
Biosynthesis).
- The "Change Current Database" tool now searches an expanded set
of organism names.
- If you create a SmartTable of BioCyc organisms, you can now use the SmartTables operation "add property column"
to examine organism metadata for the organisms. To create an organism SmartTable, go to a gene page and then click
"Change Organisms/Databases for Future Comparison Operations" in the right-sidebar menu.
- Circular Genome Viewer: This tool can now display data tracks from an uploaded GFF file.
- When searching a PGDB for chemical substructures, substructures can now be drawn using
the JSME editor (see Tools → Search → Search Compounds).
PathoLogic
- Operon predictor upgraded: The operon predictor predicts
single and multigene transcription units (operons) and adds those
predicted transcription units to the PGDB. We have developed a new model for
the process of determining where a pair of adjacent genes are either within
a transcription unit or staddle a boundary between transcription units. The
model uses GO Biological Function annotations and additional features and
logistic regression to classify the pairs. The accuracy of this prediction
model has been improved about 4 percent compared to the previous
predictor when tested on the EcoCyc database. The predictor can
also use a file of gene expression data to use correlation of gene-expression levels in the prediction model.
- Transporter Inference Parser (TIP) Upgraded: The TIP tool infers transport reactions from transporter
names, and adds those transport reactions to the PGDB. It includes a tool that enables the user to review,
approve, and modify its inferences. This latter tool has been updated for better incremental
operation, enabling the user to save their status, exit the software, and resume reviewing at a later time.
Release Notes for Pathway Tools Software Version 26.0
Released on April 14, 2022.
Navigator -- Web
- Most graphics within Pathway Tools generated web pages can now be printed to a PDF file by clicking
the printer icon that appears to the left when you mouse over the graphic. Examples of printable
graphics include genome-browser images, pathway diagrams, complete metabolic network diagrams, and the regulation summary diagrams that appear in gene pages.
- Large pathway diagrams are now scaled to fit within the web browser page; they can be zoomed
by moving your mouse into the pathway diagram and moving the mouse wheel or using the zoom controls
that appear on the left.
- A number of improvements have been made to comparative analysis operations. For example, they have been extended to support
the (relatively) new EC 7 enzyme class.
Navigator -- Desktop
- Improvements have been made to several of the Advanced Search commands, such as Gene → Advanced Search
PathoLogic
- A new simplified command-line interface for building new PGDBs has been added to PathoLogic. For example,
to create a new PGDB from the genome in a .gbff (or .gff) file and perform a metabolic reconstruction on that genome, execute:
pathway-tools -patho filename.gbff
To create a new PGDB from a gbff file and run all PathoLogic inferences (metabolic reconstruction, operon prediction (for prokaryotes only), protein-complex prediction, transport-reaction inference, and pathway hole filling) execute:
pathway-tools -patho-all filename.gbff
.gbff and .gff files are both nice in allowing you to encode multiple replicons in a single file.
In our experience .gff files are a bit better at complex cases such as multiple splice forms.
Release Notes for Pathway Tools Software Version 25.5
Released on December 20, 2021.
Navigator -- Web and Desktop Modes
- Pathway Tools now runs under MacOS Monterey
Navigator -- Web Mode
- Speedups to Regulatory Overview: We have made substantial speedups to the regulatory network viewer called the Regulatory Overview
(for EcoCyc web mode see Tools → Genome → Regulatory Overview)
PathoLogic
- New Protein Complex Inference Tool: PathoLogic includes a new tool for inferring protein complexes during processing of genomes.
The tool works by recognizing common "core strings" across multiple polypeptides within an annotated genome. For example,
the polypeptides whose names are "tryptophan synthase, alpha subunit" and "tryptophan synthase, beta subunit" share the core string
"tryptophan synthase," thus a complex would be created by the tool that contains these two polypeptides.
- Improvements to Transport Inference Parser: We have revamped the Transport Inference Parser tool that parses transporter protein names
and creates transport reactions to improve its accuracy in a number of respects.
- PathoLogic Automated Build extended to include all refinements: All PathoLogic inference tools that can run in batch mode but previously had to be invoked individually from the Refine menu in GUI mode can now be optionally included in the PathoLogic Automated Build step. These tools include the Pathway Hole Filler, the Operon Predictor, the Transport Inference Parser, and the new Protein Complex Inference Tool.
- Improvements to GenBank and GFF File Parsers: We have improved both of these parsers abilities to parse eukaryotic GenBank and GFF files.
We do recommend GFF format for importing eukaryotic genomes into Pathway Tools.
Release Notes for Pathway Tools Software Version 25.0
Released on May 26th, 2021.
Navigator -- Web and Desktop Modes
- Updates to GO Term Processing: EcoCyc has captured annotations using Gene Ontology (GO) terms
for many years. However, our software did not capture some previous complexities of GO, and
the GO file format (GAF) has undergone some changes recently, which our software did not support.
Therefore, we have extended GO support in Pathway Tools to cover the newly mandatory "qualifier"
column of GAF, including the "NOT" relation. These extensions required changes in our database
schema, in the interactive editors used by curators, the web-based display of GO annotations, and
in GO-based enrichment analyses.
Navigator -- Web Mode
- Multi-PGDB Searches: Several of the searches available under Search now enable searches across multiple organism databases (up to 70). For example,
this option enables searching across multiple strains or members of a microbial community to find which organisms contain a given gene, metabolite, or pathway. All the search and
filtering options applicable to that search are supported. The searches include
- Search Genes, Protein or RNA
- Search Compounds
- Search Reactions
- Search Pathways
- Multiple Sequence Alignment: The alignment tool at Analysis → Multiple Sequence Alignment now supports alignment of arbitrary nucleotide regions
of a replicon, and aligning user-provided sequences in addition to sequences from BioCyc databases.
- Comparative Analysis: Many improvements have been made to the comparative tools under Analysis → Comparative Analysis:
- The tools are significantly faster.
- The organism comparison provides new comparisons of phenotype metadata, collection metadata, and annotation metadata
- The reactions comparison now identifies both shared and unique reactions between organisms
- Comparisons of biosynthetic pathways now provide both a pathway view and a metabolite view that more clearly identifies which metabolites can be synthesized -- see example
- The compounds comparison now identifies both shared and unique metabolites between organisms
Release Notes for Pathway Tools Software Version 24.5
Released on Jan 15th, 2021.
Navigator -- Web and Desktop Versions
- Circular Genome Viewer: A new circular genome viewer tool provides a global view of the organization of one or more chromosomes as a set of concentric circles (tracks) containing features (genes, promoters, binding-sites, other extragenic sites) of interest.
A given track can be customized to show and/or highlight features that match specified criteria. For example, a track can be filtered to only show RNA genes, or transporters, or genes from an uploaded file. Alternatively, a track might show all genes, but highlight those involved in certain pathway classes or annotated to specified GO terms. The circular genome viewer can also be used to compare chromosomes from multiple closely related strains, such that highlights can be applied to orthologs across all strains. The circular genome viewer is accessible on the web as Genome → Circular Genome Viewer and in the desktop software as Chromosome → Circular Genome Viewer.
- Gene-Reaction Schematic: Gene and Protein pages can show
the so-called Gene-Reaction Schematic, which aims to clarify the
relations between reactions, enzymes, and their genes. Complicated
many to many relations can exist, which are difficult to understand
without a visual representation. Some reactions are even composed of
subreactions. A recent improvement to the schematic diagrams shows
the subreactions in a separate layer from the regular reactions,
thereby clarifying their roles.
Navigator -- Desktop
- Performance Improvements: Improvements have been made to speed up PGDB save operations when using MySQL for PGDB storage.
Navigator -- Web
- Metabolic Network Explorer: The new Metabolic Network Explorer facilitates the interactive exploration of the metabolic network around a set of connected compounds of interest.
To access this tool, go to Metabolism → Metabolic Network Explorer and enter a starting metabolite.
You can then build up a linear reaction path by adding successive reactions forward or backward from the current path.
For each metabolite along the central path, lists of precursor and successor metabolites provide information about other possible connections to that metabolite, and allow the user to extend or change the central path to follow one of those connections. Various customizations are supported.
- Regulatory Overview: We've upgraded the regulatory network browser (Regulatory Overview) to
utilize HTML5 canvas graphical rendering via our Webgraphics package,
yielding better quality graphics and faster zooming. See Genome → Regulatory Overview.
We also have incorporated changes that enable the user to
display successive levels of regulation one level at a time,
and to print to a file either the entire regulatory network, or the network regulated by a single gene.
- Genome Overview: Genome Overview already was using Webgraphics
for rendering, but we added the ability to highlight genes, either by
the gene name or identifier, or by highlighting those genes
whose name has a shared substring. See Genome → Genome Overview.
- Multiple Sequence Alignment: We've updated Multiple Sequence Alignment
to utilize Clustal Ω for computing the alignments and to utilize
MSAViewer for the visualization of the alignments. See Analysis → Multiple Sequence Alignment.
- Comparative Analysis: The organism comparison report now compares organism metadata.
The reaction comparison report now includes those reactions unique to each organism. See Analysis → Comparative Analysis.
PathoLogic
- Uniprot-seq-ids files: The unprot-seq-ids files, used by the
gap filler, have been enhanced with the addition of ids and sequence
data from Entrez. The naming has changed as well. We now provide
three files:
- protein-seq-ids-unreduced.dat - This file contains all the UniProt and Entrez ids
associated with each reaction.
- protein-seq-ids-reduced-70.dat - This file contains the protein ids that
remain after blast processing to remove sequences more than 70 percent
similar to other sequences in the same reaction.
- protein-seq-ids-reduced.seq - This file contains the sequences
that correspond to each id in the protein-seq-ids-reduced-70.dat file.
Protein identifiers in the files now have a prefix of either `UNIPROT:' or
`PID:', the latter indicating an Entrez identifier.
Release Notes for Pathway Tools Software Version 24.0
Released on May 22, 2020.
Changes to Navigator -- Web and Desktop Versions
- MacOS Catalina: We extended PTools to run under MacOS Catalina.
- Pathway Layout Improvements: We made a number of improvements to PTools metabolic pathway layout algorithms, including
adding compartments to pathway diagrams. Chemical structure displays were also improved.
Changes to Navigator -- Web Only
- Organism Selector: The organism selector now provides new filter options, such as for listing
all Tier 2 PGDBs, or all PGDBS for NCBI representative genomes.
Changes to Navigator -- Desktop Only
Changes to PathoLogic -- Desktop Only
Changes to MetaFlux -- Desktop Only
- New Taxonomic Gap Filler: A new gap-filling mode (TaxGap, for Taxonomic Gap-filling) has been added to MetaFlux and is set as the default mode for bacterial and archaeal PGDBs. TaxGap assigns different weights to candidate reactions based on the frequency the reaction appears in other BioCyc PGDBs at the same taxonomic level of the current organism. TaxGap has been shown to be significantly more accurate than the previous method. Learn more about TaxGap at doi.org/10.1093/bioinformatics/btz813.
Release Notes for Pathway Tools Software Version 23.5
Released on December 19, 2019
Changes to Navigator -- Desktop Only
- Multiple-Choose Menus: Please be aware that many of our multiple-choose menus now support more
modern conventions: To select a range of entries, click on the first entry and then shift-click on the last entry.
To select multiple entries individually, command-click them.
- Cell-Type Specific Metabolic Maps: The Navigator can now produce different metabolic map diagrams for
different cell types, such as to reflect the different metabolic networks active in different human cell types.
Changes to Navigator -- Web Only
- Exporting Pathway Collages to SVG files is now supported to enable higher quality images to be exported.
- BLAST search: We made several improvements to BLAST searches including adding the
ability within the BLAST search page to select a different PGDB for searching other than the current PGDB.
- Favorites SmartTable: A "Favorites" SmartTable is now defined for each user. It is accessible
through the "Add to SmartTable" button near the top of many pages.
- Pathway Evidence Report Sorted by Pathway Score: A new variant of the pathway evidence
report available from command Analysis → Reports → Pathway Evidence sorts the
report by pathway score to speed review of low-scoring pathways. Note that older BioCyc databases
do not contain pathway scores.
Changes to Editors -- Desktop Only
- Atom Mapping Editor: Pathway Tools now includes an atom-mapping editor for manually creating
and modifying the mappings of atoms from reactants of PGDB reactions to their products.
Changes to PathoLogic -- Desktop Only
- Enzyme Name Matcher Extended: The enzyme name matcher that maps enzyme names
to the reactions they catalyze draws from a large dictionary of enzyme names. That
dictionary has been extended substantially by analyzing a list of unmatched enzyme names
that frequently occur in sequenced microbes. Furthermore, the name matcher now uses gene
names to resolve ambiguous enzyme names and to assign reactions when the enzyme name is
not recognized. We have also adjusted the name matcher in a number of ways to decrease
incorrect matches.
- Improved Pathway Inference: Pathway inference has been improved through more
extensive use of "key reaction" definitions in MetaCyc pathways, and through the use of
a new feature called "key non-reactions", which prevent inference of a given pathway if a specific reaction
outside that pathway is catalyzed by the organism. In particular these new rules enable
more accurate inference of the appropriate variants of the TCA cycle and glycolysis pathways.
In addition, super pathways are now inferred more accurately.
Changes to MetaFlux -- Desktop Only
- SBML Import: The MetaFlux SBML import tool has been updated to read SBML Level 3 files with
Flux Balance Constraints (the fbc package). The tool is currently limited to
prokaryotes and will be extended to eukaryotes in the future. The SBML Importer
will attempt to merge compounds and reactions with those in MetaCyc based on
available links to identifiers in external databases (such as KEGG, BiGG, ChEBI,
InChIKey) and other chemical properties. If an objective function is detected, an option to generate an FBA file
will be available.
Release Notes for Pathway Tools Software Version 23.0
Released on April 29, 2019
Changes to Navigator -- Desktop Only
- Multi-Organism Metabolic Maps: The Navigator can now produce metabolic map diagrams for multiple organisms,
such as from a microbiome or microbial community. See Overviews → Build Community Overview.
- Multi-Organism Search: The Navigator now supports queries across multiple PGDBs, such as searching for
all PGDBs that contain a given gene or pathway. The user must define a set of PGDBs
to query across. For example, an organism set might consist of organisms from
a microbiome body site to enable the user to determine which organisms contain
a gene or pathway. To define an organism set, click on the current organism selector
right under the file menu.
- GenBank and GFF Export: The commands for exporting GenBank and GFF files now enable the user to
select which replicon(s) to export, which nucleotide range to export, and which
types of features to export. See File → Export → Selected Replicon(s) to GenBank File
and File → Export → Selected Replicon(s) to GFF3 File.
- SBML Export: The SBML exporter has been updated to level 3 version 1 with flux balance
constraints package version 2. We now support two modes of export: 1) generate SBML file for
selected reactions from a PGDB (see File → Export → Generate SBML File For... →
Selected Reactions) and 2) generate SBML file for an FBA model including the objective
function and model parameters (see File → Export → Generate SBML File For... →
Flux Balance Analysis). The latter mode can also be found in the MetaFlux dialog window.
Changes to Navigator -- Web Only
- Pathway Covering: A new metabolomics analysis operation called Pathway Covering is available.
It computes a minimal number of pathways that cover (contain) a supplied set of metabolites.
See Analysis → Metabolomics Pathway Coverage.
- Reaction diagrams in reaction pages are now formatted using our improved graphics system.
- Speed improvements have been made to most queries within the Search menu.
Changes to PathoLogic -- Desktop Only
- Speed improvements have been made to PathoLogic.
Changes to MetaFlux -- Desktop Only
- Flux Variability Analysis: MetaFlux now contains a tool for computing Flux Variability Analysis
for a metabolic model, that is the range of possible flux values that
each reaction in the model may take.
Release Notes for Pathway Tools Software Version 22.5
Released on September 27, 2018
Changes to Navigator -- Desktop Only
- Multiomics Explainer: This new omics-analysis tool leverages what is known
about an organism's metabolic and regulatory network to suggest
explanations for the results of omics experiments. An example application for
the tool is to generate mechanistic explanations for how a gene knock-out
leads to altered metabolite levels.
Querying a database such as EcoCyc, the MultiOmics Explainer searches
the organism's network of metabolic reactions, transporters,
cofactors, enzyme substrate-level activation and inhibition
relationships, and transcriptional and translational regulation
relationships, to identify paths of influence among input genes,
proteins and metabolites. Results are presented in a combined
metabolic and regulatory diagram. Invoke at Tools → Multiomics Explainer.
Changes to Navigator -- Web Only
- New Search Commands: The following new search commands have been added:
- Search for cryptic prophages via
Search → Search DNA or RNA sites → Search by site type → Cryptic Prophages
- Search for pseudogenes via
Search → Search genes, proteins, or RNAs → Search/filter by type/subunits → Pseudogenes only
- Performance Enhancements: We have engineered a number of performance enhancements,
particularly to decrease the time to generate gene pages.
Changes Common to Web and Desktop Versions
- Pseudogenes: Our internal representations for pseudogenes
have changed to provide more consistent and comprehensive treatment of pseudogenes.
Changes to PathoLogic -- Desktop Only
- PathoLogic now extracts organism metadata from its input files
(PathoLogic format, Genbank format, and GFF format) for inclusion in
a PGDB. Example metadata include the geographic location from which the organism was
sampled, its aerobicity, and its human microbiome body site.
Release Notes for Pathway Tools Software Version 22.0
Released on April 25, 2018
Changes Common to Web and Desktop Versions
- Pathway regulation: Pathway diagrams can now include
detailed regulatory information for each step that are taken from
the regulatory data present within a given PGDB. From any
pathway page, such as
L-homoserine
biosynthesis, click on the "Show Regulation Details" button
above the pathway diagram to see transcriptional, translational and
substrate-level regulators included in the diagram. This button
will only be present if there is regulation data available for the
pathway, and if the pathway is displayed at a detail level that
shows enzyme names. Mouse over any regulator icon for more
information. Mouse over regulation arrows to identify which ligands
influence specific isozymes.
- Improvements to the GlycanBuilder software and glycan pathways:
Back in 2012, we integrated the GlycanBuilder software with Pathways
Tools (Desktop Only; see Section 9.3.10 of the User Guide, Glycan Structure Editor).
The software enables drawing glycan structures using icons that depict
sugar residues, making it a lot easier to comprehend the structures of
complex polysaccharides. Utilizing these structures in glycan
biosynthetic pathways enables users to quickly grasp how a sugar
residue is added to the growing polymer. A year later, we introduced a
new type of pathway diagrams based on these structures to describe the
complex process of glycan degradation. In these diagrams, arrows
indicate where different enzymes cleave the glycan macro molecule,
enabling the description of complex processes, in which multiple
enzymes act in parallel with no particular order.
In order to make these structures more useful for BioCyc users, we
next introduced several new features to the original GlycanBuilder
code. Perhaps the most important such feature is the ability to display
text strings or other, non-glycan, compounds as part of the glycan
structure. This allows, for example, to depict how an oligosaccharide
is connected to a lipid membrane anchor or to a glycoprotein.
Unfortunately, a myriad of technical complications prevented us from
using this useful addition for several years. However, for version
22.0 of Pathway Tools, these issues were resolved, allowing us to
convert a large number of pathways to the glycan format. A few example
pathways include:
Changes to Navigator -- Web Only
Changes to PathoLogic -- Desktop Only
- PathoLogic can now accept input genomes in GFF format in addition
to Genbank format and PathoLogic format.
- We have made substantial performance improvements to some PathoLogic modules, such as speeding up
the generation of the Cellular Overview.
Changes to MetaFlux -- Desktop Only
- The computational technique used for the MetaFlux general development mode
(for gap-filling a metabolic model) --- Mixed-Integer Linear
Programming (MILP) --- has been modified to enhance its accuracy. The new
technique enforces the biomass reaction flux to be at least 0.001,
while at the same time still supporting the possibility of not being
able to produce some of the biomass metabolites. Previously, the
gap-filling of reaction networks did not enforce the minimum biomass
flux of 0.001 when some of the biomass metabolites were given as
"try-biomass". The previous technique was generating more gap-filling
solutions that would not show growth than the new technique. The
following paper describes the previous and new techniques:
"Evaluation of reaction gap-filling accuracy by randomization,"
Latendresse M., Karp PD., BMC Bioinformatics 2018 19(1):53.
Release Notes for Pathway Tools Software Version 21.5
Released on December 1, 2017
Changes Common to Web and Desktop Versions
- Omics Dashboard: The Dashboard is an interactive tool for
exploration and analysis of gene-expression and metabolomics datasets
(see Dashboard publication in Nucleic Acids Research).
For more information see the Dashboard Help document and
Webinar #7 describing the Omics Dashboard.
New features added in this version include the following.
- Extended the list of top-level panels to include several panels of non-metabolic functions including a panel for sigma factor regulons
- "Show Genes Not Present in any Subsystem" button generates a list of genes not mapped to any panel
- Added ability to search for a given gene by name and have the Dashboard open the panel hierarchy to show that gene (see Search link at top of page)
- The experiment legend is shown at top of every pane
- New options for creating publication-quality diagrams:
- "Hide Controls" option removes all option buttons. The user can also now hide the control panel accordion on the right of the page.
- User can now specify y-axis legend
- "Hide Panel" command is now present in every panel's Options menu to unshow the panel
- Regulator panel: added disjunction option, added list of regulators to tooltip for gene
- Handle multiple replicons when sorting by map position
- Put tooltips on the genes in the operon diagrams, and made the diagrams clickable
- Add ability to generate empty dashboard for explanatory purposes
- Added "Panel Description" command to panel Options menu to let users find out which GO terms are being used to define a given segment within the dashboard
- Pwy diagrams: color scheme cutoff now computed only from data in diagram.
- When generating pathway collage from dashboard image, keep user-specified color scale
Changes to Navigator -- Web
- Omics Pop-ups Use Google Charts: Previously the Omics Pop-ups used Adobe Flash, but
as Flash is no longer supported by some browsers, we have re-implemented the Omics Pop-ups using
Google Charts.
- Improved Graphics and Fonts: We have upgraded many additional Web visualizations
produced by Pathway Tools in its web server mode to use modern graphics and fonts,
including the genome browser; genome overview; transport reactions; operon diagrams; transcription-unit diagrams;
functionally-linked gene cluster diagrams;
gene-neighbor diagrams; mapped-genes diagram;
protein features; and sequence diagrams for promoters, binding-sites, and attenuators.
Changes to Navigator -- Desktop
- Omics Viewer Data Import from Metabolomics Workbench: The Cellular Omics Viewer has been extended
to import metabolomics data from the Metabolomics Workbench.
The interface is similar to that used to import expression data from GEO.
See Overviews → Omics Viewer: Overlay Experimental Data From → Metabolomics Workbench.
- GFF File Export: Pathway Tools can now export the genome information within a PGDB
in GFF file format. See File → Export → Entire PGDB to GFF3 Format.
Release Notes for Pathway Tools Software Version 21.0
Released on May 3, 2017
Changes Common to Web and Desktop Versions
Changes to Navigator -- Web
- Improved Graphics and Fonts: We have upgraded some of the visualizations
produced by Pathway Tools in its web server mode to use modern graphics and fonts,
such as the Regulation Summary Diagram on gene pages.
- Multi-Organism Metabolic Route Search: The metabolic route search capability
has been extended to enable searches across organism communities (see
Metabolism → Metabolic Route Search). The expanded route-search tool
can be used to answer the question:
how does the human gut microbiome convert compound X to compound Y? First select
the set of organisms whose metabolic reaction sets will be considered in the search --
the set of gut-microbiome organisms can be selected by using the Organism Properties
tab of the organism selector, and requesting organisms whose Human Microbiome Body Site
has the value gastrointestinal-tract. Next select the starting and ending compounds,
X and Y. The tool will search for lowest cost routes between X and Y, through a
metabolic reaction network consisting of the union of metabolic reactions in all
BioCyc organisms defined as residing in the human gut. Individual organisms can
be specified as well.
Release Notes for Pathway Tools Software Version 20.5
Released on December 17, 2016
Changes Common to Web and Desktop Versions
- Revised Protein Feature Coloring: We have revised the coloring
scheme within the protein-feature display to assign a fixed set of colors
to different feature types. For example, all enzyme active site features
will be colored purple.
- Performance improvements: We have made substantial performance improvements to
the Ocelot database management system that underlies Pathway Tools, including
decreasing the memory usage of the BioCyc web servers.
Changes to Navigator -- Web
- Receive Notification of Database Updates -- This new facility, present only in BioCyc.org, allows scientists to sign up to be
notified of curation of new information in their research interest area(s). Sign
up via the Update Notifications Page
(available through Analysis → Update Notifications)
to be notified when new curation (which indicates new published experimental findings) occurs
for specific genes or metabolic pathways. You can also sign up for notifications in interest
areas specified by Gene Ontology terms, such as cell motility or cell division -- you will
then be notified whenever new curation occurs in genes involved in those biological processes.
Notifications will be
sent by email in conjunction with BioCyc releases.
- https: Pathway Tools web servers can now operate using the secure https protocol.
If you are interested in enabling https, please contact us.
- Expanded Organism Searches: The "search by organism properties" option within the
organism selector menu in the upper-right corner of most BioCyc pages
includes additional searches to
enable users to find BioCyc databases based on the amount of data of different types present
in the database, including:
- Number of Gene Ontology terms
- Number Phenotype Microarray datasets
- Number of gene essentiality datasets
- Number of genes with essentiality data
- Number of transcriptional regulatory interactions (i.e., size of regulatory network present)
Changes to Navigator -- Desktop
- Set Default Organism -- You can now define a default organism that will be selected
whenever you launch Pathway Tools using Tools → Preferences → Preferred Database.
Changes to Editors
- We added support for Chemaxon's MarvinJS molecular structure editor,
which is a Javascript based replacement for the Marvin applet, given
that many Web browsers are deprecating Java applets.
Release Notes for Pathway Tools Software Version 20.0
Released on May 19, 2016
Changes Common to Web and Desktop Versions
- Gene/reaction schematic improvements: The gene/reaction schematic diagram has been
improved to reduce the size of large tangled sets of gene-reaction relationships by truncating such diagrams. A button is now
provided to allow the user to toggle between full and truncated versions of the diagram.
- Performance improvements: We have made substantial performance improvements to PathoLogic and to
the Ocelot database management system that underlies Pathway Tools.
- Pathway Perturbation Scores: The option to generate a table of pathways overlaid
with omics data now ranks pathways by Pathway Perturbation Score, a new
score that attempts to measure the overall average degree to which the
reactions in a pathway are perturbed over the course of an omics
experiment. From the website Metabolism → Cellular
Overview page, select "Upload Data from File" and ask to
show the data as a table of pathway diagrams.
Changes to Navigator -- Web
- Metabolic and genome posters for all BioCyc organisms are available -- see the commands
Metabolism → Generate Metabolic Map Poster and Genome → Generate Genome Poster
- Re-designed metabolite pages: BioCyc metabolite pages have been re-designed to
structure metabolite information across multiple tabs to make information easier to find and assimilate.
- Search for DNA sites: The new command Search → Search DNA or mRNA Sites enables searches
for sites such as promoters and attenuators, potentially filtering by replicon, nucleotide coordinates, and ligands.
- New Cellular Overview highlighting commands: Several new commands are available to help you
find information within the Cellular Overview (metabolic map) diagram. Under the right-sidebar menu,
see these new commands:
- Highlight reaction by enzyme cellular location
- Highlight reaction by modulation (finds reactions according to substrate-level regulation of enzyme activity)
- Highlight enzyme by curation
- Sequence coordinate mapping service: This new service at Genome → Map Sequence Coordinates enables mapping of data files
containing genome coordinates across different versions of the genome coordinate systems that arise
when a genome sequence is updated. Currently, EcoCyc is the only genome in BioCyc that contains multiple
coordinate-system versions.
- Improved command to Search for Reactions by Substrates: This command, which enables users to
search for reactions by specifying one or more substrates, now enables users to specify which side of the reaction different substrates are on, relative to each other (see Search → Search Reactions).
- New Pathway Collages page: The new page Metabolism → Pathway Collages enables users to generate a Pathway Collage by selecting from a list of all pathways in the current database.
Changes to MetaFlux Metabolic Modeling Tool
MetaFlux has undergone the following enhancements:
- Run metabolic models using web interface: You can now run metabolic models in BioCyc with a few mouse
clicks, as follows:
- Find BioCyc organisms with metabolic models by clicking "change organism database", then select the
tab "Having Metabolic Models". Click the organism for which you want to run a model and click OK.
- Then run command Metabolism → Run Metabolic Model and follow the instructions.
- Example: Click here to run the EcoCyc metabolic model.
- Models are available on BioCyc.org for two other gut-microbiome bacteria.
Release Notes for Pathway Tools Software Version 19.5
Released on November 18, 2015
Changes Common to Web and Desktop Versions
- New pathway collage feature: A pathway collage is a diagram depicting a set of connected metabolic
pathways, possibly with omics data superimposed (example here). You can now interactively create a pathway collage in
Pathway Tools desktop and Web modes. To create a pathway collage in Web mode:
- (Optional) Load a gene expression or metabolomics data file if you want to include
such data within your collage, by bringing up the cellular overview (Metabolism → Cellular Overview)
and then running Right-Sidebar Menu → Overlay Experimental Data (Omics Viewer) → Upload Data from File.
- Specify the pathways to include in the collage in one of two ways:
- Go to any pathway page and then invoke Right-Sidebar Menu → Generate Pathway Collage.
- Create a SmartTable containing the pathways to include in the collage and then invoke
Right-Sidebar Menu → Export → Export Pathways to Pathway Collage.
- The collage will be created in your web browser,
where you will be able to reposition the pathways interactively, add additional pathways to the collage,
add connections between metabolites, change various
display styles, and view omics data, to create your desired diagram. Export the diagram to a file for
inclusion in a publication. For more details see the Website User's Guide.
Changes to Navigator -- Web
- Redesigned gene pages: We have redesigned the Web gene pages for a more modern
look and to make information easier to find. Gene pages now contain a series of tabs; clicking
on a given tab shows a specific type of information, such as the reactions catalyzed by a
gene product, the GO terms assigned to the gene, or the features defined for the gene product.
Note that the set of tabs present varies depending on the type of the gene product and the
information available. The "Show All" tab combines all information in one page for easier
searching.
- New Cellular Overview queries: New Web Cellular Overivew right-sidebar menu query operations include:
- Highlight Genes → By replicon and By Regulon
- Highlight Reactions → By Evidence
- Highlight Pathways → By Curation and By Evidence.
- Many performance improvements and bug fixes have been made to SmartTables.
- Performance improvements have been made to Search → Cross Organism Search.
Changes to PathoLogic
- Metabolic Pathway-Prediction Algorithm Revamped: The pathway prediction algorithm has undergone a
major revision to increase its accuracy. The new algorithm makes use of a new pathway score, which is a measure of
the likelihood that a pathway is present. The pathway score depends on scores from each reaction in the pathway,
which depend on factors such as whether an enzyme catalyzing the reaction is present, how many pathways
a reaction is present in, and whether the reaction is annotated as a "key reaction" for predicting the pathway.
More details: PathoLogic chapter of the Pathway Tools User's Guide.
Changes to MetaFlux Metabolic Modeling Tool
MetaFlux has undergone the following enhancements:
- Dynamic FBA: MetaFlux can now perform dynamic FBA in addition to the previous steady-state FBA.
In dynamic FBA, a steady-state metabolic model can be executed across multiple time steps.
Dynamic FBA can be applied to single organisms or to organism
communities to predict changes in organism abundance over time.
New nutrients and organisms can be introduced at specific grid points and specific times during a simulation.
- Model a spatial grid: Models can now be executed across a user-defined rectangular
grid in addition to the previous single spatial compartment. Diffusion of cells and small molecules
is simulated across the grid.
- New graphical outputs: MetaFlux is tightly integrated with
GnuPlot so that model results can be visualized in several ways such as
viewing the time course of organism biomass changes and metabolite concentration changes, both
overall, and across the grid. Results can be viewed as static X-Y plots and as MetaFlux-generated videos.
Release Notes for Pathway Tools Software Version 19.0
Released on March 25, 2015
General Changes
- Genome browser: The Pathway Tools genome browser now depicts transcription factor binding sites and
attenuators, and will display the nucleotide sequence at high magnification levels.
Navigator -- Web
- Sequence variant data analysis: Web SmartTables support a new analysis operation for sequence variant data.
The user can define a SmartTable of replicon regions and associated sequence variants
via a file import operation.
Then, the SmartTables transformation
"Sequence -- nearest gene to DNA region" adds
additional columns to the SmartTable showing the nearest gene to
each region, and the amino-acid change caused by each sequence substitution.
MetaFlux Metabolic Modeling Tool
- Blocked reactions: The MetaFlux log file now includes a listing of
blocked reactions. These reactions must always carry zero flux, given a set
of nutrients, secretions and biomass metabolites. More precisely, a (basic) blocked reaction has at least
one reactant that is not produced by any reaction, and is not a
nutrient; or has at least one product that is not consumed by any
reaction, and is not a secretion, and is not a biomass metabolite. A blocked reaction is a basic
blocked reaction or a reaction that becomes blocked by iteratively
removing basic and blocked reactions from the model. A basic blocking metabolite
creates a basic blocked reaction. In the log file, the list of
all blocked reactions are grouped based on the basic blocking
metabolites. This grouping helps inform the user why some reactions are blocked in a model.
- Reaction taxonomic range in gap filler: The MetaFlux gap filler (development mode) adds new reactions to a metabolic model to make
the model solvable. The cost of adding a reaction depends on whether the expected taxonomic
range of the reaction is consistent with the current organism. Previously, only reactions in
pathways had taxonomic range information. Now, taxonomic information is computed for as many
reactions as possible based on the taxonomic groups of the known UniProt proteins that catalyze the reaction.
- Display of reaction fluxes: When displaying reaction fluxes computed by MetaFlux on the Pathway Tools metabolic map
diagram (the Cellular Overview), two new capabilities are available:
- When the mouse pointer is moved over a metabolite in the Cellular Overview, a pop-up window lists the
fluxes through all reactions that consume and produce the metabolite.
- A new control panel allows you to enable a mode in which clicking
on a metabolite node in the Cellular Overview with incoming or
outgoing flux draws connections between that node and all other nodes for
that metabolite that have complementary flux. When run in development
mode, the control panel also lists all reactions suggested for import.
Clicking on any such reaction shows in the Cellular Overview how the
addition of that reaction would connect existing fluxes.
Editors
- Sequence Editor: A new interactive sequence editing tool is available for making manual updates to a replicon sequence. See Chromosome → Edit Nucleotide Sequence.
Release Notes for Pathway Tools Software Version 18.5
Released on Nov 11, 2014
General Changes
Navigator -- Desktop
- The SBML exporter was augmented to include many more database links to external
database resources, in a format that is commonly used by the COBRA
Toolbox. Also included are a confidence level for annotations, and gene--reaction association
information.
- It is now easier than ever to display omics data on pathway pages, with a
new command to upload data onto a pathway, and an omics control panel that
remembers the latest dataset as you navigate from one pathway to another, and
allows you to turn on or off the omics display.
Navigator -- Web
- Quick Search locus IDs: The Web quick-search box now accepts an additional search option: enter a gene
locus ID from any BioCyc genome, regardless of the currently selected organism.
Example: entering MSM_0046 will find an NADH oxidase in Methanobrevibacter smithii.
- Omics popups on pathway pages: The pathway customization options have been extended to support upload of omics datasets with multiple timepoints, displayed using omics popups. Visit any pathway page and choose the "Customize or Overlay Omics Data on Pathway Diagram" operation.
MetaFlux
- Metabolic models of organism communities: MetaFlux now supports construction of quantitative metabolic models for communities of
organisms, such as bacteria within the human microbiome.
- Inference of biomass metabolite list: MetaFlux can now generate a suggested biomass metabolite list
for many organisms by using biomass compositions recorded for nine different taxonomic groups.
Editors
- The PGDB Info Editor has been extended to support entry and updating of organism phenotype data
such as the temperature range and aerobicity of the organism via the MIGS (Minimal Information
about a (Meta)Genome Sequence) standard.
Release Notes for Pathway Tools Software Version 18.0
Released on March 13, 2014
General Changes
Navigator -- Desktop
- Quicksearch: The new desktop quicksearch toward the bottom left of the screen
is analogous to the web quicksearch: it performs a substring search with the user's input
word(s) against the names of most entities in the current PGDB, including genes, compounds,
and pathways.
- SBML Import Tool: A new tool allows you to import an SBML file into a new or existing PGDB.
The tool creates all metabolites and reactions defined in the SBML file in the PGDB, and
attempts to map those metabolites and reactions to metabolites and reactions in MetaCyc.
See File → Import → SBML into DB....
Navigator -- Web
- Cross-Organism Search: This new tool enables name-based searches across specified
sets of organisms in BioCyc. For example, you can search a specified taxonomic group in BioCyc
(e.g., all cyanobacteria) for metabolites (or proteins, or pathways)
having a certain substring in their name (e.g., achromobactin).
See Search → Cross Organism Search.
- Sequence pattern searches: You can now search a genome for exact or degenerate
short patterns of nucleotides or amino acids.
See Search → Sequence Pattern Search.
- Sequence alignments: You can now obtain multiple sequence alignments
for genes and proteins, both within a genome and across genomes.
See Search → Sequence Pattern Search.
See on gene pages Right Sidebar Menu → Align gene nucleotide sequence with orthologs
and a similar command for proteins.
- Groups / SmartTables Enhancements:
- Groups have been renamed to SmartTables.
- Given a SmartTable containing genes or proteins, you can invoke a multiple sequence
alignment for those genes or proteins
- A single SmartTable can now hold objects from multiple databases
- The SmartTable right-sidebar menus have been re-organized.
- The icons in column headers have been re-organized with some options moved to the right-sidebar menus.
A new collapse-column option is available.
- Several performance improvements have been made for large SmartTables
- Added support for peptide regions as a SmartTable object type
MetaFlux
- Compartment-Based Gap Filling: MetaFlux can now handle metabolic models with multiple compartments in a more
precise and flexible way, for solving or for gap-filling. We added
11 special keywords to specify sets of reactions that are active in
specific compartments to describe a model or as candidate reactions to
try to add to the model (gap-filling). For example, a user can
describe a model for the mitochondrial lumen by specifying
"metab-compartment[mitochondrial lumen]" for the set of metabolic
reactions of the model. Transport reactions to and from a specific
compartment, or via a membrane, can also be specified using similar
special keywords. For gap-filling a model, it is possible to specify
sets of metabolic and transport reactions defined in MetaCyc so that
sets of candidate reactions can be used to gap-fill a model for
specific compartments.
Release Notes for Pathway Tools Software Version 17.5
Released on October 15, 2013
General Changes
- Creation and Editing of Glycans and Glycan Pathways: New
in this version is the ability to create pathways containing glycan
compounds that are depicted using icons for the sugar residues. The
pathway diagrams include arrows that indicate where degradation
enzymes act on the large, polymeric glycan structures. Pathway Tools
interfaces with the GlycanBuilder applet to enable editing of glycan
structures. The GlycanBuilder applet is now bundled with Pathway
Tools, so no additional installation effort is necessary. This also
includes SRI changes to the applet that are not yet available from the
official download site.
Example pathway: xyloglucan degradation I (endoglucanase)
Navigator -- Desktop
- Interface to OPM Phenotype Microarray software:
OPM
is a software package for manipulating and analyzing Biolog Phenotype Microarray data.
Pathway Tools can now import
Phenotype Microarray data into a PGDB from a discretized OPM YAML file.
Once imported, such data can be displayed using previously existing Pathway Tools functionality.
- Desktop Cellular Omics Viewer:
- Gene expression data can now be retrieved from PortEco and from GEO
- Labels for pathway groups are now included in the Overview diagram
Navigator -- Web
- General Web Interface Improvements:
- The menubars for BioCyc, EcoCyc, etc have been re-organized for improved accessibility
- The previous object-specific menus have been replaced by a right-sidebar menu of operations
that changes depending on what type of page the user is visiting
- Web Cellular Overview and Omics Viewer: This tool has undergone a major overhaul including
- It runs much faster and many bug fixes have been made
- Gene expression data to be displayed on the Cellular Overview can now be retrieved from PortEco, from GEO, and from Web Groups
- Pop-up improvements
- Many new search commands are available
- Labels for pathway groups are now included in the diagram
- Groups Enhancements: A number of enhancements have been made to both Web Groups
including:
- Groups can now be published. Once published a group is publically readable, and
the group cannot be deleted, even by its owner. The idea is to encourage scientists to
refer to published groups in their scientific publications.
- Users can now create temporary groups without creating a BioCyc account to
facilitate experimentation with Groups.
- Database identifiers in database links can be added as groups columns, e.g., KEGG IDs for
BioCyc compounds.
- A group of objects can be created via text entry.
- New row selection operations are available.
- The star in the heading of the first column allows the user to toggle between
viewing object names and object identifiers.
- New Web Services: See the web services documentation page
for more details about the following new web services.
- Retrieve the BioCyc ID of a BioCyc object given its identifier in a foreign database, e.g., a UniProt ID
- Retrieve a BioCyc compound given a monoisotopic molecular weight and a tolerance value
- New Ways of Creating Web Links to BioCyc: See the BioCyc linking documentation page
for more details.
- Link to BioCyc proteins via UniProt ID
- Link to BioCyc genes via the Accession-1 and Accession-2 slots
MetaFlux
- New Fast Development Mode: MetaFlux includes a new Fast Development Mode (FDM)
that can perform reaction gap filling much faster than the previous General Development Mode (GDM).
However, FDM cannot gap fill on secretions or nutrients as GDM can, nor does FDM tell
the user which biomass metabolites cannot be produced by an FBA model.
Release Notes for Pathway Tools Software Version 17.0
Released on March 29, 2013
General Changes
- Support for 32-bit Linux Discontinued: Because 64-bit Linux machines have been
the standard for several years now, we have discontinued the release of the 32-bit Linux version
of Pathway Tools.
- Groups Enhancements: A number of enhancements have been made to both Web Groups
and Desktop Groups including re-organization of Web Groups menus and addition of new transformations.
- Rate-Limiting Reactions: A reaction can now be designated as rate limiting with respect to
a given metabolic pathway, using the pathway editor. Rate-limiting reactions are identified
as such in pathway diagrams using an hourglass icon.
Navigator -- Desktop
- PGDB Registry Speedups: The PGDB registry is a facility whereby Pathway Tools
users can share and download PGDBs via the Internet. As the number of PGDBs in the registry grew, the speed
of the registry became far too slow; the registry interface has been re-designed so
that finding PGDBs within the registry is much faster.
Navigator -- Web
- Web Omics Pop-ups: When using the Cellular Omics Viewer you can
view a graph of omics data (e.g., plotting gene-expression data over time for
a given gene). To do so, paint expression data on the Cellular Overview.
Then mouse over a reaction (or metabolite) of interest. Click "Omics"
in the menu of the resulting pop-up window, which will graph the omics
data for that reaction.
RouteSearch -- Metabolic Route Search
The new Web-based RouteSearch tool, accessible from command
Tools → Metabolic Route Search, supports two types of searches in metabolic
networks. For both types of search, the user specifies a starting and ending
metabolite of interest, and the software generates alternative reaction
pathways connecting those metabolites. For more details see the
Metabolic Route Search section of the Web Site User's Guide.
- Mode 1 -- Within Organism Searches: In this mode the search
makes use of reactions within the selected PGDB only.
- Mode 2 -- Synthetic Pathway Searches: In this mode the search
makes use of reactions within the selected PGDB plus reactions within the
MetaCyc DB. The user may specify a higher penalty for introducing
reactions from MetaCyc. This mode is not available within public
Pathway Tools web servers but may be accessed by installing Pathway
Tools locally and running a web server accessible on an intranet.
PathoLogic
- Pathway Abundance Scores for Metagenome Data: PathoLogic can now compute abundance
scores for pathways based on gene abundance values provided in a .PF input file.
Gene entries in a .PF file may contain ABUNDANCE fields that specify the number of
times that gene was observed in a metagenomics dataset. The abundance scores are
present in file pathways-report.txt in the PGDB reports directory. More information on calculation
of abundance scores will be provided in a future blog post.
- Enzyme Name Matcher: The enzyme name matcher assigns enzymes to MetaCyc reactions during the reactome
inference stage of pathway prediction. We have made extensive improvements to
the name matcher that increase its sensitivity (recognition of enzyme names) with
little if any decrease in its specificity.
MetaFlux
- Several performance and user interface improvements
were made to MetaFlux.
Internals
Improvements to Pathway Tools internals include:
- Web images are now cached for longer time periods to increase performance, rather than being deleted on each
restart of the Pathway Tools web server.
- A new library called Skippy is used for Web image generation, replacing the older GD,
which did not work on Windows-64. (The Lisp-based Skippy is faster than the C-based GD.)
- A new cross-platform installer is used for Pathway Tools.
- The performance of the Pathway Tools MySQL database interface (PERK) has been improved
in several respects.
Release Notes for Pathway Tools Software Version 16.5
Released on November 15, 2012
General Changes
- MacOS 10.8: Pathway Tools 16.5 works under MacOS 10.8; previous versions of Pathway Tools do not.
- Phenotype Microarrays and Other Growth Data: The displays of growth media, growth
observations, and phenotype microarray data has been substantially
revised. Tables for growth observation data on gene and growth
medium pages now include aerobicity and osmolarity information. The
page describing all growth media has been revamped with improved
colors and clearer indications (both in the tables and in the
tooltips) of precisely what growth observation data is available.
This page includes a new option to generate a heatmap to, for
example, show how gene knockouts affect growth on different nutrient
sources. Information about display of growth media and growth
observations can be found in the Growth Media Page section of the
Pathway Tools User Guide.
Bulk Upload of Growth Observation Data: Two new tools are
available for the bulk upload of growth observation data to a PGDB from a
spreadsheet file. To import essential gene data for a particular
growth medium, use the desktop command Edit → Import
Knockout Data from File in the right-click menu for that growth
medium. To import phenotype microarray data for a particular PM
plate, use the desktop
command File → Import → Phenotype
Microarray Data from Spreadsheet.
- Atom Mappings: Atom mappings define the correspondence between atoms in the reactants
of a chemical reaction, and the atoms in the products of that reaction. MetaCyc now contains
atom mapping data for thousands of reactions. Pathway Tools uses that atom mapping data to
color conserved moieties within chemical reactions, both within MetaCyc and for mapped MetaCyc reactions
present in other PGDBs. For more information see Section "Atom Mappings" in the
PGDB Concepts Guide.
- Chemical radicals: Pathway Tools now supports chemical radicals.
- New representation of EC Numbers in Pathway Tools: The Enzyme Commission
(EC) classifies enzymes based on the reactions they catalyze. Since EC numbers
are issued for enzymes and not reactions, a single EC number can be associated
with multiple reactions, and on the other hand, a single reaction can be
associated with multiple EC numbers. Until now, EC
numbers were assigned in Pathway Tools to the reactions, with a limitation of
only one EC number per reaction. Starting with version 16.5, EC
numbers are represented by a new type of object within Pathway Tools PGDBs. For most reactions (those
with just a single EC number) the main difference on the reaction page is that the EC
number at the top of the page is now mouse-sensitive. Clicking on the EC number
navigates to a new type of Pathway Tools page, the EC-number page. The difference is more obvious if a reaction is associated with multiple
EC numbers. In these cases all of the EC numbers, along with their names, comments, citations,
etc., appear on the reaction page. Similarly, visiting the page for an EC number that
is associated with multiple reactions will enable the user to see all the
reactions (and enzymes) that are associated with it. In addition, from now on, an
enzyme will only be associated with an EC number if it is known to catalyze all of the
official reactions (if there are more than one) associated with that EC number.
Web Mode Only
- Many Web Groups Enhancements:
- Many new transformations have been added and many transformations have been renamed. New
transformations include:
- New regulation transformations for genes
- Transform gene to upstream promoter
- Transform protein to DNA sites it binds to
- Transform compound to proteins that bind to or are activated or inhibited by that compound
- Nucleotide and amino-acid sequences can be added as group columns for genes and proteins.
Genes, promoters, and transcription factor binding sites can be transformed to their DNA
region (coordinates) or to their sequence.
- You can import a list of DNA regions or points from a file (e.g., mutation locations) to
form a group. That group could be transformed to the set of genes nearest those regions.
See Groups → New → Group from File of Replicon Coordinates.
- Customize Pathway Diagram with Omics Data: The command Pathway → Customize Pathway Diagram
now includes an option for painting omics data onto an individual pathway diagram.
- Web Omics Viewer Displays Table of Pathways:
The Cellular Omics Viewer (see Cellular Overview → Overlay Experimental Data)
now includes an option previously present in the desktop version, namely to generate a table
displaying omics data painted onto diagrams of individual pathways. This option can be selected
from the "Show data:" selector in the Omics Viewer dialog.
Desktop Mode Only
- MetaFlux for Windows: The MetaFlux component of Pathway Tools for building
steady-state metabolic flux models now runs under Windows in addition to Linux and Mac.
- Save Display State: You can now save the display state of Pathway Tools for later
restoration by you or by someone you send a display-state file to. Examples
of display state you can save include the state of the omics viewers (including
omics pop-ups), genome-browser tracks, and cloned windows. See File → Save Display State to File
and the complementary restore command.
- Captions in Cellular Omics Viewer: You can add captions for elements of the
Cellular Overview diagram by right-clicking on a metabolite or a reaction and selecting
Show Caption.
- Glycan Structures: Pathway Tools now supports display and editing of
glycan structures.
Glycan compounds may now contain two types of structures: the traditional atomic
structure, and a glycan structure that uses icons that depict sugar residues. The latter allows a
more compact visual representation of large glycans, clarifying the essential
structural features. Curation of the new iconic structures has been enabled
by interfacing Pathway Tools to the Glycan Builder Java applet (see
Section 9.3.10 "Glycan Structure Editor" User Guide).
Release Notes for Pathway Tools Software Version 16.0
Released on February 21, 2012
Web Mode Only
- Pathway Tools web server mode now works for the Windows-64 platform.
- Improve chemical graphics: The graphic display of chemical structures on compound and reaction pages has
been re-implemented using the SVG web standard, resulting in higher quality graphics.
(This improvement is currently visible only using recent versions of Firefox.)
- New multi-organism selector: A new multiple organism selector dialog is now available when performing comparative
operations, such as using the comparative genome browser, and showing information about
a given gene or pathway across multiple organisms. The new dialog is much faster and easier to use than the older selector page.
- A spelling corrector is now used during web searches.
- Highlighting large groups: Previously, when painting a group (such as a gene group) to the web Cellular Overview, only short groups (of length < 100)
were supported. Now this operation will work for arbitrarily long groups.
Desktop Mode Only
- MetaFlux FBA Module Available on More Platforms: MetaFlux now runs on MacOS, and it runs on
older versions of Linux-64 than it did previously.
- Enzyme Editor: An option was added to the enzyme editor to link the enzyme to an
additional reaction, optionally copying non-kinetic fields
(e.g. cofactors, inhibitors, citations, comments, etc.) from an
existing enzyme activity. It is now also possible to mark an enzyme
activity as not physiologically relevant.
Release Notes for Pathway Tools Software Version 15.5
Released on October 25, 2011
General Changes
- Growth Medium Search: The new command Search → Growth Media (Tools → Search → Growth Media in the desktop software) enables
searching for growth media in the current PGDB according to several criteria.
- Improvements to Generic Reactions: Generic reactions in PGDBs are reactions
whose classes are substrates, such as "an alcohol" and "an L-1-phosphatidyl glycerol."
Improvements in the handling of generic reactions include display of such reactions
on compound pages.
Web Mode Only
- Web Object Groups: A web implementation of the object
groups facility now exists. Users can define groups of objects of
interest (such as a list of genes or metabolites), either by entering
them manually or by defining groups from query results. Users can
operate on web groups in a variety of ways, such as painting all
objects in a group on an overview diagram, or transforming an object
group (such as transforming a group of one or more genes to a group
containing the one or more pathways involving those genes).
Enrichment analyses can be performed on object groups (such as
determining whether a gene group is over-represented for a set of
pathways or a set of Gene Ontology terms). Object groups can be
private, or users can share object groups with other specific users,
or make them public. See Tools → Groups and the
Groups Webinar.
Note that Pathway Tools web accounts must be enabled to run web groups.
- Taxonomic Organism Selector: The web "change organism database" dialog now provides
a new mode of selecting organisms by taxonomic group; click on the "By Taxonomy" tab at the
top of the selection dialog.
- Improved Nucleotide Sequence Selector: The web button "Nucleotide Sequence, Advanced"
on gene/protein pages has been improved to allow specification of the desired sequence
in terms of absolute coordinates as well as relative coordinates upstream and downstream of
the starting gene.
- New Web Services: Many of the Pathway Tools API functions have been made available via the web services interface. See the appropriate section in the Website User Guide for more details.
One application using the Pathway Tools Web services is the bioCycPlugin for Cytoscape.
- Performance: Many performance improvements have been made to web server mode.
Desktop Mode Only
- MetaFlux FBA Module Supports Gene Knock-Outs: The PTools FBA module has been extended
to support prediction of growth or no-growth for single and double gene and/or reaction knock-outs.
See the FBA chapter of the User's Guide for more details. This module predicts growth/no-growth for E. coli with an accuracy of 86.1%.
- 64-bit Microsoft Windows Now Supported; 32-bit Windows No Longer Supported:
This and future releases of Pathway Tools will support the Windows 64-bit platform; the
Windows 32-bit platform will no longer be supported because memory layout issues
were preventing the software from working reliably on the 32-bit platform. Operation
under Windows-7 has also been improved in several respects. Please be aware of the
following current limitations of the 64-bit Windows version:
- In this version 15.5, Pathway Tools web server mode does not currently work for Windows-64. We hope to have
this problem fixed for the next release or sooner.
- Improved Control Over Compound Connections in Cellular Overview: A new dialog
provides finer control over what connections between metabolites are displayed in the Cellular
Overview. To enter the dialog, right-click on a compound in the Cellular overview and select
Compound → Display Connections for this Compound.
Release Notes for Pathway Tools Software Version 15.0
Released on March 22, 2011
General Changes
- Pathway Layout:
We made many improvements to our pathway layout algorithms, resulting
in pathway diagrams that are more pleasing and more compact.
- Dead-End Metabolite Finder: An interactive tool for finding dead-end metabolites is available. Dead-end metabolites
are metabolites that are either only produced by the reactions of the metabolic network,
or only consumed by those reactions. Most dead-end metabolites are indicative of
omissions in the metabolic network model.
Desktop: Tools → Dead-end Metabolite Finder
Web: Tools → Dead-end Metabolites
- Choke-Point Finder: An interactive tool for choke-point analysis of metabolic networks is available.
Choke-point reactions are singleton reactions that produce or consume a metabolite,
and may represent good anti-microbial drug targets.
Desktop: Tools → Choke-point Reaction Finder
Web: Tools → Choke-point Reactions
- Find by Curation Status: New commands have been added to find pathways and proteins by curation status, meaning
the degree of curation they have undergone:
Overviews → Highlight → Pathway → By Curation Status
Overviews → Highlight → Reaction → By Curation Status
Pathway → Search by Curation status
Protein → Search by Curation status
- Omics Viewer Color Scales:
We have changed the color scales in the omics viewers to improve them
from a human factors perspective. More improvements may be released
as patches in the near future.
- Reaction Compartments: The Pathway Tools internal representation of reaction compartments has been
changed substantially to provide a more compact and expressive representation
of the locations of enzymatic and transport reactions through a new slot
on reactions called Rxn-Locations.
Web Mode Only
- Paint Pathways via Web Services:
It is now possible, using a web services interface, to paint omics
data from a file onto a set of pathways of interest on a Pathway Tools
website, displayed in table form (one or more timepoints), or on a
regular pathway display (one timepoint only). For more information,
see the section "Submitting Expression Data Via an HTTP GET or POST
for Display on Individual Pathways" in the Website User
Guide.
Desktop Mode Only
- Generate Metabolic Flux Models: The new MetaFlux component of Pathway Tools can now generate metabolic flux models using
flux-balance analysis, using a methodology that greatly reduces the
time needed to construct such models. These models are automatically
generated from a PGDB, and sent to an optimization program for
solving. The computed steady-state fluxes can be displayed on the
Cellular Overview. If no flux solution is found, we provide a
"multiple gap filling" approach to aid in debugging the metabolic
model. The software postulates additional reactions from MetaCyc that
if added to the PGDB will produce additional biomass compounds; it
postulates additional nutrients that if added will allow the network
to produce additional biomass compounds; and it indicates what subset
of the biomass compounds cannot be produced. See Chapter 8 of the User's Guide.
- Groups Enhancements: Several enhancements have been made to the object groups facility:
- The user can define a group from an omics data file, and select those genes that are
up-regulated OR down-regulated by some factor (previously only one of the preceding
choices could be made, whereas now both sets of genes can be selected within one group).
- Given a list of genes and associated omics data (e.g., expression data), the desktop
command Groups → Transform Group → Significant Pathways of Genes will generate a
new group consisting of those pathways whose genes show an average expression above
a user-specified value, or that contain at least one gene whose expression is above
a user-specified value.
- Growth Media Editor: Pathway Tools now contains an interactive editor for creating and
modifying descriptions of growth media (see File → Create → Growth
Medium), and growth media display pages are now provided. The list of
growth media present in a PGDB are listed at the bottom of the table on the
organism summary page.
- SMILES Parser: The Pathway Tools SMILES parser has been significantly rewritten and enhanced;
its wildcard syntax now conforms with SMARTS
(see http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html).
- Web Cellular Overview: Regeneration of the Cellular Overview diagram (which occurs in desktop
mode) now also regenerates the image tile files needed by the Web
version of this diagram. This regeneration can take a long time
(e.g., 10 minutes or more), so it is best to do it offline rather than
on an active website.
Release Notes for Pathway Tools Software Version 14.5
Released on October 10, 2010
General Changes
- New Regulation Summary Diagram: Gene pages now contain a diagram that summarizes
all regulatory influences on the gene as described in the PGDB. For example, the
EcoCyc gene page for bglG
shows the influences of transcription factors, attenuation, and post-translational
modification of the gene product.
- Performance Improvements: The speed of Pathway Tools has
been significantly increased in a number of areas. For example,
PathoLogic will now process large data files (such as for metagenomics)
roughly 5 times faster, and SAQP and BioVelo queries are significantly faster.
Web Mode Only
- New Web Services: Pathway Tools based Web servers such as BioCyc.org
now support an array of Web services that enable Web-based retrieval of PGDB data
such as data for a gene or pathway. [Details]
- New Monoisotopic Mass Search to Support Metabolomics:
The Search → Compounds page now contains a
filter for searching for compounds by monoisotopic molecular weight, which
is useful for analyzing mass spectroscopy data.
- Faster Web Cellular Overview: The recent re-implementation of
the Web Cellular Overview has been reworked to significantly increase
its speed. The Cellular Omics Viewer speed has been increased, and the dialog
for invoking the Omics Viewer has been simplified.
Tooltips for this diagram have been improved -- these
pop-up windows can be moved, and kept, and multiple such windows
can be opened simultaneously.
- Omics Viewer available for Web Regulatory Overview: The
Omics viewer is now available for the Web Regulatory Overview, and the
speed of the Web Regulatory Overview has been increased significantly.
Desktop Mode Only
- The dialog window for invoking the Omics Viewers has been simplified.
- Highlight by Evidence Codes in Cellular Overview: The user can
highlight reactions or pathways within the Cellular Overview according to
their evidence codes, such as highlighting all pathways with experimental evidence. See for example command
Overviews → Highlight → Pathway → By Evidence
- Molfile Support for V3000 format: Pathway Tools can now read and
write V3000 Molfiles, allowing it to handle chemical structures containing
more than 1,000 atoms.
- Orthology-Based Multi-Strain Gene Editor: A new editor
is available that allows propagation of annotations across multiple
genes based on orthology. The editor is intended to be used when
curating multiple strains of an organism. It allows visual comparison
and propagation of gene names, product names, GO terms, and reaction assignments.
Use of this editor requires some special configuration; please contact us
if you are interested in trying it.
- Mac Installer Improved: The Mac installer has been improved in
several respects, for example, it will now download needed X-Windows libraries
automatically.
- Configuration of MySQL Server: The new command
File → Configure New DB from MySQL allows
a user to configure a connection from their copy of Pathway Tools
to one or more PGDBs stored in a specified MySQL server.
It is to be used for establishing such a connection for the first time.
Release Notes for Pathway Tools Software Version 14.0
Released on March 22, 2010
General Changes
- Signaling Pathways: Pathway Tools now contains an
interactive editor for signaling pathways, and the Navigator can
display signaling pathways created using that editor. The editor can be invoked
through the desktop command Pathway → New → Signaling Pathway.
See User Guide Section "Signaling Pathway Editor".
Click here for an example human signaling pathway.
- New Web Cellular Overview: A new implementation of the
Web Cellular Overview exists. This implementation, based on modern
Web technologies, allows zooming and searching of the diagram in
a similar manner to the functionality available on the desktop
version of the diagram. See Web Toolbar command
Tools → Cellular Overview.
For documentation see command Cellular Overview → Help.
- Combined Gene/Protein Pages: The formerly separate
gene and protein pages have been unified into a single page,
in order to avoid confusion about what information resides on
what page, and to reduce unnecessary navigation.
Example: E. coli argA.
Desktop Mode Only
- All Enrichment Analysis: The enrichment analysis tools
within the Groups menu now include an All option that will search
all ontology terms simultaneously for enrichment, rather than
requiring the user to search only one set of ontology terms.
- TIP Persistence: The Transport Inference Parser within
PathoLogic now allows the user to exit while reviewing TIP
predictions, and to then re-run TIP at a later time to continue
reviewing the predictions.
- Progress Bars: Progress bars are now available
for many parts of Pathway Tools.
- Memos: Users can save text notes, called memos, to any
PGDB object. Memos will be displayed in the information page for that
object, e.g., the gene/protein page. Memos can be saved for
user-created PGDBs and for read-only built-in PGDBs such as EcoCyc and
MetaCyc. Memos persist across new versions of Pathway Tools. The
user must set up a separate MySQL server for storing Memos. See User
Guide Section "Memos".
Release Notes for Pathway Tools Software Version 13.5
Released on October 13, 2009
General Changes
- Genome browser improvements:When displaying external
data tracks, a new bar graph mode was added, which fills the
rectangular area between the horizontal line and the baseline
(corresponding to the score zero) with a solid color. This mode is
useful for features that are very narrow, which might otherwise be
hard to see. In the graph modes, a single color is assigned to each
track. The color can be chosen by adding a special header comment
into the GFF file, to allow users to follow their own color
conventions. Many common colors can be specified, using this syntax
(without quotes): "##color green" . The original graph mode was
changed to show scores as horizontal lines spanning the length of the
features, instead of showing a dot in the center. On the desktop
version, the ordering of the tracks can be changed. In the graph
modes, score values that fall outside the selected range are visually
indicated. Error reporting of syntactic problems in the GFF files has
been improved.
- Improved documentation for PTools API: A new document has
been prepared to better describe the API (programmer interface) for
accessing Pathway Tools programmatically from Lisp, Perl, or Java. The
PTools API document can be viewed online here: http://brg.ai.sri.com/ptools/api/
- Explicit gene accession numbers:Rather than being stored
in the synonym fields, up to two gene accession numbers can now be stored
for each gene within fields called ACCESSION-1 and ACCESSION-2, which
are accessible through the Editors.
- Reaction direction improvements:The REACTION-DIRECTION slot is
now available also for reactions, in addition to enzymatic-reactions.
In reactions, a directionality can be directly stored as a value, or
otherwise, a value will be computationally inferred, taking into
account information recorded in the enzymatic-reactions, usage in
pathways, and some special case reaction types. The reaction editor
allows directly setting this slot in reactions, and a consistency
check upon exiting the editor will check for conflicts with inferred
values, if any.
- FASTA files in the exported flatfiles: protseq.fasta was renamed to
protseq.fsa, and contains the amino acid sequences for all
protein-coding genes in a PGDB. The new file dnaseq.fsa was added,
containing the nucleotide sequences for every gene in the PGDB.
Web Mode Only
- Web Regulatory Overview: The Regulatory Overview diagram that depicts the
transcriptional regulatory network of an organism is now available through the
Web. See toolbar command Tools → Regulatory Overview for
an organism database that has regulatory data (e.g., E. coli).
- Quick search enhancements: Make your quick searches more precise as follows.
By default a quick search for a term such as "argA" returns a list of all
genes, proteins, pathways, compounds, etc that contain that string as a substring.
By including additional qualifiers in the search, you can further constrain the
search to go directly to the information page you want. For example, by searching
for "argA type:gene" you will go directly to the gene page. If you prefer an
exact search to a substring search, add the qualifier search:exact. Example: "argA search:exact".
The search and type qualifiers can be combined in one search.
- Find Current Object in Other Database: From a protein page,
new toolbar commands
are available that allow you to display the equivalent protein(s) from one
or more other databases in this Web site. Similar functionality is available
for genes, pathways, reactions, and compounds.
See these toolbar commands:
- Protein → Show This Protein in Another Database (equivalent object found based on orthology and name search)
- Protein → Show This Protein in All Databases (orthology and name search)
- Gene → Show This Gene in Another Database (orthology and name search)
- Gene → Show This Gene in All Databases (orthology and name search)
- Pathway → Show This Pathway in Another Database (frame-id search)
- Pathway → Show This Pathway in All Databases (frame-id search)
- Peaction → Show This Reaction in Another Database (frame-id search)
- Reaction → Show This Reaction in All Databases (frame-id search)
- Compound → Show This Compound in Another Database (frame-id search)
- Compound → Show This Compound in All Databases (frame-id search)
- Web server performance improvements: A number of improvements have been made to speed up
the operation of the new Pathway Tools Web front end released in version 13.0. These
improvements include implementation of server data compression, and ability of the
server to keep TCP connections alive across multiple requests from a Web browser.
Desktop Mode Only
- Manipulation of Object Groups for Omics Data Analysis: A new
facility is available for manipulating groups of objects, such as a
group of genes that are up-regulated in a gene expression experiment,
or a group of metabolites that are up-regulated in a metabolomics
experiment. The facility allows users to define and store a group of
objects, to transform them into another group (such as to transform a
gene list into a list of pathways containing those genes, or into an
expanded list of genes that includes all genes in the same operon as the
original genes), and to perform over-representation analysis on a
group. See the Groups menu and Section 3.8.13 of the Pathway Tools User's Guide.
- Omics data graphing capabilities: The Omics Viewers now have the
capability to show a graph of the set of data values (such as for a
time series experiment) for a given object or set of objects (such as
all the genes in a pathway) in a small popup overlay that the user can
drag to reposition as desired. The graph can be customized to display
either as a heat map, a bar graph or a plot. In addition, the
software remembers the most recently loaded omics dataset so that these
graphs can be added to any object display (such as for genes in an
individual pathway display). To show the omics graph popup, right
click on any object (such as a gene or reaction in any of the Omics
Viewers, or a reaction in a pathway display). If there is omics data
associated with that object, the menu will include the command "Show
Omics Data in Popup". In the Cellular Overview, this command will
also appear in the Pathway submenu, which shows the graph for all
the objects in the pathway. Right-clicking on any omics graph popup
allows you to change the display preferences.
- UniProt Protein Feature Import Tool: Pathway Tools now has the ability to import protein features from UniProt into a Pathway/Genome Database. This import tool works by connecting either to the PublicHouse installation of the BioWarehouse (www.biowarehouse.org), or to your own local installation. See command File → Import → Import Protein Features from UniProt.
Changes to Editors
- Protein editor upgraded: The protein editor now contains
multiple tabs, with different tabs for subunits, enzymatic activity
and modified forms. New modified forms of a protein can be created
directly from within the protein editor. The protein subunit
structure editor now permits editing of a protein with arbitrarily
nested substructure (i.e. a complex of complexes).
Release Notes for Pathway Tools Software Version 13.0
Released on March 10, 2009
General Changes
- Agricola: PGDBs now support references to publications in the Agricola
bibliographic database. Citations using Agricola IDs can now be used in the same
way as PubMed IDs are used, such as in the citations slot. Example
Agricola citation: [IND20337009].
Web mode only
- Major upgrade to Pathway Tools Web server mode: The Web interface of
Pathway Tools has undergone a major upgrade. The old Pathway Tools
query page (server.html) is no longer recommended for use. It has been replaced by
a three-tiered system of searches that includes
a new quick search box, and by a new toolbar that appears at the top
of every Web page. The toolbar contains a Search menu whose
functionality subsumes all the functionality of the previous query
page. A short video tutorial on the new Web interface is
available here. If you are running a Pathway Tools Web server,
you will probably want to customize it as described in Section 8.3
of the Pathway Tools User's Guide.
- The Pathway Tools Structured Advanced Query Page (SAQP)
has been enhanced in several respects.
- Regular expression searches on strings can be done using two
new operators. It is using Perl regular expression syntax.
- The number of non null values of attributes are displayed in the attribute selectors.
This gives an indication of how much data the database has for particular attributes.
- The output result of a query can now be sorted on any column without resubmitting the query.
This can be done by clicking small triangles in the column header of the table.
- Subqueries using quantifiers introduce variables. It is now possible to refer
to these variables in the output specification.
Desktop mode only:
- BioPAX 3.0: Pathway Tools is now able to import and export data using the
BioPAX Level 3.0 standard.
- Printing improvements:
- Windows only: Users can now print directly to a printer rather than to files only.
Note that printing under Pathway Tools for Windows depends on Ghostscript and GSview.
Both programs must be installed on the Windows computer. Ghostscript and GSview installation
instructions are provided in the Pathway Tools Installation Guide.
- Linux only: The print dialog now allows the user to choose from a list of
available printers rather than having to specify the printer via a command line.
- All platforms: The user can now select printing to PDF files in addition
to the previous option of PostScript files.
- Network Reachability Analysis: Pathway Tools now includes a tool that performs reachability
analysis of the metabolic network within a PGDB. Reachability
analysis is a method for validating a metabolic network model by
identifying gaps and errors within the network, and is an
important prerequisite for other modeling methodologies such as
Flux Balance Analysis. The user begins
by defining a known (or hypothetical) growth medium for the organism,
as well as a set of compounds that the organism is expected to be
able to synthesize from those growth medium (e.g., the cellular
building blocks). The software then computes whether, starting
from that growth medium, the metabolic reaction network is capable
of producing the expected product compounds. If it cannot,
graphical debugging tools are available to allow the user to
determine where are the gaps in the metabolic network.
The tool is accessible as Tools→Reachability Analysis.
- Regulatory Overview: The Regulatory Overview has been enhanced in several respects.
- There is a new layout called "Straight Rows Layout"
that displays the genes in rows from top to bottom
such that the genes that regulate the most number of genes tend to be at the top
and no gene in a row directly regulates another gene in the
same row. By default, this layout is
used when using the command Overviews→Redisplay Highlighted Genes Only.
Although, the choice of the layout can be changed
via the regulatory overview preferences using the command
Overviews→Preferences For Regulatory Overview. For example, the entire
regulatory overview can be displayed using this layout by selecting
it for the preference "Layout for Complete Overview".
- After selecting a set of genes using one of the search functions, it is now possible to also display
the regulatory relationships between them.
- Shift-Left displays object in new window: A new shortcut is available for displaying object pages in a
separate pop-up window. Hold down the Shift key while left-clicking
on an object name (such as a pathway name) in a Pathway Tools display
to display that pathway in a new pop-up window rather than in the
main Navigator window.
- Creation of relationship links:
Any of the editors where database links can be entered now include the ability to select the type of relationship that the link represents.
Changes to PathoLogic
- PathoLogic now properly recognizes non-coding RNA entries in Genbank files
(ncRNA features) and creates corresponding RNA objects in the PGDB.
Release Notes for Pathway Tools Software Version 12.5
Released on October 16, 2008
General Changes
- Electron transfer pathways: Pathway Tools is now able to edit and display
electron-transfer pathways consisting of coupled electron-transfer
reactions. Example pathway:
NADH to cytochrome bd oxidase electron transfer.
- Regulation: small RNAs: Pathway Tools now supports the ability
to edit and display regulatory processes mediated by small RNAs. Example:
RyeE small RNA.
- Tips system: Pathway Tools now contains a system for periodically
providing tips on Pathway Tools usage to users. We have found that
many users are unaware of many Pathway Tools capabilities, and we
hope this will be an effective educational device.
- Pathway reference lists: A new reference list at the bottom of each
pathway page includes all references cited in the pathway, and
in all enzymes belonging to the pathway.
- Propagate MetaCyc updates to your PGDB: A new tool is available that
will propagate updates made to the MetaCyc PGDB to PGDBs that you have created.
For example, when you create a PGDB, its reactions and compounds are copied from
MetaCyc. But over time, corrections are made to MetaCyc, such as correcting
chemical structures and balancing chemical reactions. The new tool will
propagate those corrections to your PGDB. For more information see Section 6.8 of
the User's Guide: "Updating for New Versions of MetaCyc".
Web mode only:
- Customize pathway diagrams for Powerpoint or publications:
Pathway pages now contain a Customize Diagram button.
Click it to generate a customized drawing of the
pathway by setting parameters that control how pathway drawings
are produced. Options include setting the font size, what elements
are present in the drawing (such as enzyme names and gene names), whether
chemical structures are displayed, etc. Diagrams can be generated
as GIF images for import into Powerpoint, and as postscript or PDF
files for import into documents.
- Many improvements have been made to the
Structured Advanced Query Form
that allows users to construct complex queries against PGDBs.
Desktop mode only:
Changes to PathoLogic
- GO term processing: PathoLogic will now make use of Gene Ontology (GO) terms when
performing enzyme-to-reaction assignments. GO terms are used for
reaction assignment in addition to enzyme names and EC numbers
supplied for a protein. PathoLogic also checks for and reports on any
inconsistencies found between the GO terms, enzyme names and EC
numbers for each protein. GO terms are supplied in the gene/protein
entries within PathoLogic-format files, whose format is described in the
User's Guide.
Release Notes for Pathway Tools Software Version 12.0
Released on April 1, 2008
General Changes
- Macintosh port. We have ported Pathway Tools to the Macintosh. In this first version of the
port, only the Navigator and Editors are supported. PathoLogic is not supported. We expect
to add support for PathoLogic in a future version.
- New multi-platform installer. All Pathway Tools platforms now use the same
new installation tool, allowing for a consistent installation approach on all platforms.
- Incorporation of genome annotation updates. A new tool
supports the user in merging a new, external genome annotation into a
PGDB. The tool can be useful for incorporating a new version of a
genome annotation into a PGDB. The new annotation is supplied as a
PathoLogic-format file. The annotation update tool detects all
differences between gene and protein information in the supplied file
and that in the PGDB, and presents those differences interactively.
The user interactively controls which differences are incorporated
into the PGDB, and which are rejected. After the annotation update is
complete, PathoLogic can be executed to re-evaluate metabolic
pathways. New pathways will be added to the PGDB if either (a) They
are new to MetaCyc since the last time PathoLogic was run and have
sufficient evidence, or (b) They were previously not predicted as
present because of insufficient evidence, but now the presence of
additional enzymes provides sufficient evidence, or (c) They were
previously manually deleted from the PGDB but now have additional
evidence because of the presence of additional enzymes. The user is
shown all new pathways and given the opportunity to accept or reject
them. This tool can be invoked through the PathoLogic command
Build→Update Build for Revised Annotation, and is documented
in Section 6.3.8 of the User's Guide.
- New tracks mechanism for ChIP-chip data. A new X-Y plot style of
tracks for the Pathway Tools genome browser allows the user to visualize
ChIP-chip datasets against the genome. ChIP-chip intensity measurements
can be visually correlated with promoters, gene positions, and operon
boundaries. For more information see Section 3.8.11 of the User's Guide.
- Attenuation. Pathway Tools has been extended to encode six
mechanisms of attenuation. The Editors have been extended to support
curation of these attenuation types, and each type is displayed appropriately
on operon diagrams and on transcription unit pages.
- NCBI Taxonomy integrated into Pathway Tools. The NCBI Taxonomy DB
is now integrated into all Pathway Tools versions that include the MetaCyc DB. This
change was made for several reasons including allowing specification of the
taxa in which MetaCyc pathways occur using NCBI Taxonomy, and allowing querying
of MetaCyc pathways using NCBI Taxonomy (see command Pathway → Search by Organism).
- Modified GO term presentation. On protein pages and gene pages, the
presentation of GO terms has been moved and restructured so that terms are
sorted within the three domains of the Gene Ontology.
- Improved storage of sequences and overview graphs. This
improvement is relevant only for PGDBs stored in a MySQL or Oracle
relational DBMS. We have extended this PGDB storage mechanism so that
the nucleic-acid sequence data and cellular overview data are now
stored in the relational database. In the past, these data were
stored in files that had to be manually replicated on the computer of
every person accessing the PGDB in desktop mode. Now that replication
is no longer required.
- New configuration parameters. A number of new configuration parameters
have been added to ptools-local/ptools-init.dat. The file will be updated
to contain the new parameters after you have run the new version of Pathway Tools.
Check for new variables that may be relevant to your work. For example, if you
operate a Pathway Tools based Web site, there is a new parameter that lets you
enter the name of your Web site (e.g., "MouseCyc"), for use in messages and in
Web pages generated by Pathway Tools.
Desktop mode only:
- Highlight genes in Genome Overview. The Genome Overview
now includes a command Overview→Highlight Genes by Substring, which
will highlight in the diagram all genes whose name or synonyms contains
a specified substring.
- New refresh command. The new command Tools→Pane→Refresh Panes
will redraw the Navigator window in cases where it may have become corrupted.
- Improvements to metabolic map poster. The metabolic map poster than can
be generated from a PGDB has undergone several improvements including the addition of pathway class labels to
pathway groups, and improvements to the positioning of text.
Web mode only:
- Web accounts system. The Pathway Tools
Web server now includes a mechanism whereby users can create accounts
through the Web. These accounts provide a way of registering the
people who use a Pathway Tools operated Web site. Once an account is
established, users can define preferences that control the appearance
of Pathway Tools generated Web pages. The user accounts can also
store configuration information such as organism lists used in the
comparative genomics tools, and settings for the omics viewers.
User accounts are stored in an external MySQL database. This facility
is disabled within Pathway Tools Web servers unless you explicitly
turn it on. For details, see Chapter 8 of the User's Guide.
- User access control. Using a facility separate from the Web accounts
system, it is possible to limit the accessibility of some or all PGDBs within
a Pathway Tools Web server to users who are authorized through a supplied file
of user names and passwords. For example, the Pathway Tools administrator could
allow some PGDBs within their Web site to be available with no restriction, but
limit access to other PGDBs to specified lists of users. For details, see
the descriptions of the -passwd-file and -acl-file options in Section 2.3.1 (Command Line Arguments) of the Pathway Tools User's Guide.
- Advanced Query Page. The Advanced Query Page has undergone a number of
improvements, bug fixes, and optimizations.
- Species Comparison on the Cellular Overview. The Cellular
Overview Diagram available through the Web can be used to highlight
reactions shared with other organisms.
- Genome Overview now available in web mode. When invoking the Web-based
omics viewer, the user can specify that omics data should be displayed using the
cellular overview, the genome overview, or both.
- Hyperlinkable Omics Displays. Omics Viewer displays are
now accessible via the HTTP GET method, with the datafile specified as
a URL or file on the server, which means that web developers can now
generate hyperlinks that generates an omics display with a supplied
omics datafile and set of parameters. For more information, see
Section 2.4.5.1 of the User's Guide.
Changes to PathoLogic
The PathoLogic enzyme name matcher that assigns enzyme names to
MetaCyc reactions has been significantly extended to do a much smarter
generation of multiple alternative names from the starting enzyme
names found in the genome sequence. The improved version should find
more true-positive matches and fewer false-positive matches. In
addition, we are adding many additional enzyme names to MetaCyc. The
combination of these two efforts should significantly improve
PathoLogic's assignment of enzyme names to MetaCyc reactions, and the
pathway prediction process itself. Also, alternative name generation
is now applied when checking whether an enzyme name is
non-specific. This can result in fewer probable enzymes being
presented to the user in the "Assign Probable Enzymes" step of PGDB
refinement.
Release Notes for Pathway Tools Software Version 11.5
Released on August 15, 2007
General Changes
- We have completed the first phase of an effort to endow Pathway
Tools the capability to represent and manipulate information about a
wide range of cellular regulation. In this first phase, we designed a
new database schema for regulatory information, and we retrofited
Pathway Tools existing mechanisms for manipulating information about
the regulation of transcription initiation to work with this new and
expanded regulatory schema. For example, Pathway Tools components for
displaying and editing operons have been reworked to use the new
regulatory scheme, as have tools for displaying and editing
substrate-level regulation of enzyme activity. These changes required
changes in the format of the Pathway Tools flat file dumps as described below.
In more detail, the new representation is as follows. A new
Regulation class has been created, with subclasses for substrate-level
enzyme regulation and regulation of transcription initiation, as well
as for several other forms of regulation. Each regulation frame forms
a link between a regulator and a regulated entity (via the slots
REGULATOR and REGULATED-ENTITY). The MODE slot specifies whether the
regulatory effect is activatory or inhibitory.
For enzyme modulation, the regulated entity will be an
Enzymatic-Reaction frame. The MECHANISM slot of the Regulation frame
specifies whether the modulation is allosteric, competitive, or any
one of a number of other controlled vocabulary terms. These
regulation frames replace the old ACTIVATORS-* and INHIBITORS-* slots
(e.g. ACTIVATORS-ALLOSTERIC, INHIBITORS-COMPETITIVE, etc.), which are
now deprecated.
For regulation of transcription initiation, the regulated entity will
typically be a promoter, and the regulator will be a transcription
factor. The new slot ASSOCIATED-BINDING-SITE links to the
binding-site for the transcription factor. This obviates the need for
the binding-site/transcription-factor and promoter/RNA-polymerase
complex frames that were part of the previous representation, as well
as the DNA-binding-reactions that formed them, and all such complex and
DNA-binding-reaction frames have been deleted. A new slot,
BINDS-SIGMA-FACTOR, has been added to the Promoters class to indicate
which sigma factor(s) are involved with transcription initiation at a
given promoter. Since a given DNA binding site may regulate multiple
promoters, the locations of the binding sites have been converted to
absolute positions (as opposed to relative to a promoter), and the new
slot ABS-CENTER-POS replaces the old slots REGULATED-PROMOTER and
RELATIVE-CENTER-POSITION, which are now deprecated.
A new flat file, regulation.dat describes all Regulation objects, with
the attributes as described above. The files promoters.dat,
dnabindsites.dat, proteins.dat, enzrxns.dat and compounds.dat have all
been changed also to the extent necessary to incorporate the above
changes.
These schema changes allow for the representation of additional forms
of regulation as well, which will be introduced in the next Pathway
Tools release in early 2008.
- Pathway Tools has new support for representing, editing, and
displaying electron transport information. The newly introduced
Electron Transport Reactions (ETRs) are used to represent the electron
transport processes that occur in membrane-associated enzyme
complexes, involving membrane-bound electron carriers. These
processes are important for energy generation by the cell, by using
high energy electrons carried in certain substrates to increase the proton
gradient across the membrane. A new graphical diagram for an ETR
visually conveys the key features of such processes, like the
direction of the electron flow and the cell compartment locations of
where the substrates are transformed.
To capture the complex processes in at least some detail, and to reuse
recurring subreactions, ETRs are represented as novel composite
reactions that are composed of Redox Half Reactions (RHRs). RHRs have
a numerical standard reduction potential value associated with them,
which determines the direction of the electron flow. The left and
right side substrates of the ETR are inferred computationally from the
RHRs used to construct the ETR. The Reaction Editor was augmented
with 2 new modes, to allow creating and editing of RHRs and ETRs.
Support for ETRs is still somewhat experimental, and while several
examples are present in EcoCyc, more extensive curation will occur for
the next release. Feedback is welcome.
- The Pathway Tools genome browser now has a zoom bar near its navigation
control to facilitate larger changes in magnification of the genome view.
Desktop Mode Only:
- A number of improvements have been made to the Regulatory Overview
released in version 11.0.
- A tooltip window now appears on mouseover of active regions of a display.
Web Mode Only:
- Many reliability improvements have been made to Pathway Tools, in particular
to its Web mode.
Changes to PathoLogic
PathoLogic now uses a stricter form of pruning to eliminate during the
pathway prediction process pathways that are likely to be
false-positive predictions. Metabolic Pathways in MetaCyc are marked
with the taxa in which the literature tells us that those pathways are
likely to be present, called the taxonomic domain of the pathway.
When PathoLogic predicts the presence of a MetaCyc pathway in an
organism outside that taxonomic domain, stricter evidence (in terms of
number of enzymes present in the pathway) is required to retain that
pathway during the PathoLogic pathway pruning phase, than for a
pathway that has been predicted within its taxonomic domain.
Release Notes for Pathway Tools Software Version 11.0
Released on March 23, 2007
General Changes
- New Genome Overview. This tool
provides a one-screen view of every gene on one or more chromosomes
and plasmids, and can display omics data across those entire
replicons. The current version works in desktop mode only, through
Overviews→Show Genome Overview. In the next release of Pathway Tools,
the Genome Overview will work through the Web as well. To see the
Genome Overview, click here.
(See User's Guide Section 3.8.2.4.)
- New Regulatory Overview. This tool
displays the transcriptional regulatory network of an organism that is
defined in a PGDB. The network can be interrogated in several ways,
such as highlighting all genes under a specified Gene Ontology class,
and highlighting all genes regulated by a specified transcription
factor. The current version works in desktop mode only, through
Overviews→Show Complete Regulatory Overview. In the next release of
Pathway Tools, the Regulatory Overview will work through the Web as
well. To see the Regulatory Overview, click here.
(See User's Guide Section 3.8.2.3.)
The Regulatory Overview depends for its operation on an encoding of
the organism's transcriptional regulatory network within a PGDB.
Currently, EcoCyc is the only BioCyc PGDB that contains such a
regulatory network. PGDB authors can define such a network manually
using the interactive editors within Pathway Tools.
- Specify enzymes not used in pathways. A new slot Enzymes-Not-Used complements slot Enzyme-Use. The new slot allows
a curator to specify enzymes that are known to not be used in a given metabolic
pathway. This slot is accessible through the Pathway Info Editor.
- Catalytic domain protein feature. A new type of protein feature called a catalytic domain allows a PGDB
to specify what region of
a protein catalyzes which reaction of the protein. This type of feature is particularly useful for multifunctional proteins.
These features may be created through the protein editor.
- Automatic patch loading. Whenever Pathway Tools starts up, it now performs its Instant Patch command,
so that users will always be running the latest set of patches. This change
has negligible impact on startup speed. But if needed, this behavior may be
disabled by removing the option "-patch" in the script file pathway-tools under
the aic-export/pathway-tools/ptools/* sub-directory.
- Compound display coordinates are now integers rather than real numbers to
improve performance. Conversion to the new format is performed automatically
when you open a PGDB under Pathway Tools 11.0.
Changes to the Pathway/Genome Navigator
- Tracks in genome browser. The Pathway Tools genome browser now supports tracks, in a manner
similar to other genome browsers. Tracks allow genome regions defined
in a GFF input file to be graphically highlighted in the genome
browser. For more information see Chromosome→Add External Track and
Section 3.8.11 of the User's Guide.
- Metabolite tracing. A new metabolite tracing tool allows you to visually trace the path of substrates
through the metabolic network within a PGDB, using the Cellular Overview diagram.
To see an example of metabolite tracing, click here.
(See User's Guide Section 3.8.2.10.)
- Monitor sizing. Through both the desktop and Web versions, Pathway Tools now knows the size of
your monitor. For example, this allows you to create very large genome browser
displays by reshaping your Web browser to the full screen.
- Display of protein features on protein pages has been improved.
- Gene ontology assignments (both GO and MultiFun) are now displayed on
gene-product pages in addition to gene pages.
- Line wrapping of publication references has been fixed.
- Gene-reaction schematic displays in MetaCyc are broken into different
sections for each organism.
Desktop mode only:
- New commands Proteins→Search by GO Term and Proteins→Search by MultiFun Term are available.
- The cellular overview diagram can now highlight items stored on the Answer List
Web mode only:
- New BioVelo Query Language. We introduce a new advanced
query language for querying PGDBs called BioVelo. BioVelo replaces
the old Advanced Query Page. Users can construct BioVelo queries
interactively through the BioCyc Advanced Query Page [documentation], and
they can construct textual queries using BioVelo language [documentation].
- Google searching. The Navigator query page now contains a section for performing a Google-based
search of the PGDB, which uses Google's index of a PGDB to perform arbitrary
text searches against the PGDB. By default, this is enabled only for
installations that serve from port 80. If you serve from another port
and wish to add this search box, or if you serve from port 80 but your
site is not indexed by google, you can change the default behavior
with the command-line arguments -google-text-search or -no-google-text-search.
- New All-Search box. An All-Search box is now present at the bottom of every PGDB web page to allow
users to perform a new search without first clicking to the query page.
- Name mouse-overs. Mouseover of compounds, genes, and proteins will additionally
show all object synonyms.
Changes to the Pathway/Genome Editors
- Enzyme name editing. A button Edit Enzyme Name has been added to the Protein Editor to
allow the enzyme name (as separate from the enzyme activity name) to be
edited directly, and to clarify precisely when this should be done.
See section 7.6.3.5 of the User Guide for more notes on this.
- External databases. The editors now contain a command for creating or editing the
descriptions of external databases for use in PGDB links to those
databases. New databases can be added with the command
File→Create→External Database. Existing database records can be
edited by right-clicking on any link to that database and selecting
the command Edit External Database Info.
Changes to PathoLogic
None.
Release Notes for Pathway Tools Software Version 10.5
Released on September 12, 2006
General Changes
- Ontology upgrade for signaling interactions: The Pathway Tools ontology has been enhanced in several respects to
provide better support for the types of molecular interactions involved
in signaling pathways. When you open your existing PGDBs under
Pathway Tools 10.5 for the first time, their schemas will be automatically upgraded
to reflect these changes.
- Consistency checker: A set of tools are now available to perform consistency checking and
computation of cached data, for a PGDB. The consistency checking tools
search for many common types of malformed data within a PGDB, and report their
findings through a graphical interface. In many cases the tools repair
these malformed data automatically. In other cases, the user must repair
the data manually, but is guided in how to do so by the tools.
In a number of cases, PGDBs cache data that are computed from other data within the PGDB.
For example, a PGDB can cache molecular weights computed from the amino acid
sequence of the organism, and can cache bulk statistics about the PGDB such
as the number of pathways and enzymes. Tools are provided for recomputing
these data based on the current state of the PGDB.
These tools are accessed through the command Tools→Consistency Checker.
Changes to the Pathway/Genome Navigator
Desktop mode only:
- Generate metabolic map poster: Pathway Tools can now automatically generate a poster-size version of the cellular overview diagram
from any PGDB that includes the names of pathways, enzymes, genes, and metabolites. The diagram
is generated as a postscript file using the command Overview→Print as Poster.
- Generate genome poster: Pathway Tools can now automatically generate a genome map poster
using its genome browser, for any replicon in a PGDB. The diagram is
generated as a postscript file using the command Chromosome→Print poster of chromosome.
- Zooming in overview: The Pathway Tools overview diagram now has semantic zooming capability -- as the user zooms to higher magnifications, first arrowheads, then pathway and metabolite names, and finally enzyme names appear.
- Sequence retrieval tool: A new tool for retrieving regions of nucleic acid sequence for a given
replicon has been implemented. It is available through the command
Chromosome→Show Sequence of a Segment of Chromosome
- BioPAX export: A new desktop-mode command is provided called File→Export→Entire DB to BioPAX file
Web mode only:
- Pathway page BioPAX: Buttons are now provided on pathway display pages to generate for a
given pathway:
- The BioPAX-format encoding of the pathway
- A list of all genes in that pathway
Changes to the Pathway/Genome Editors
- New reaction editor: The Pathway Tools Reaction Editor has been completely reimplemented to
provide a more intuitive interface for editing biochemical reactions. In addition to
providing the ability to enter metabolic reactions and transport reactions,
the new Reaction Editor can also edit reactions involved in signal-transduction
pathways. This editor is a major step toward full support for signaling pathways
within Pathway Tools.
- Compound duplicate checking: The Compound Editor now checks if a newly created chemical compound is a duplicate of
an existing compound in either the current PGDB or in MetaCyc, by searching both
the names and chemical structure of the new compound.
- Spelling checker: The Pathway/Genome Editors now include a spelling checker that
is run on text fields such a comments. It is temporarily disabled
until a small glitch is fixed, at which point it will be enabled
via a patch. Watch for a "spell check" button near comment
entry panes, such as in the protein editor.
Changes to the PathoLogic
The Pathway Hole Filler is now fully functional under the Windows
operating system.
Release Notes for Pathway Tools Software Version 10.0
Released on March 15, 2006
General Changes
- Support for Gene Ontology.
Pathway Tools now provides display, editing, and schema support for Gene Ontology.
Users can assign Gene Ontology terms to genes within a PGDB using
the Pathway Tools gene editor.
- New author crediting system.
This new system within Pathway Tools allows curators to annotate pathways
and proteins with information about who curated and reviewed
these data within a PGDB, and when literature searches were last performed.
Information about last curation and review dates are displayed within
Pathway Tools display pages, and provide a way of crediting collaborators
who assist with PGDB curation. Information about last literature-search
dates are useful for tracking how up to date are annotations within a
PGDB, and what entities should be curated next.
- Improvements to relational database support. The Pathway
Tools distribution containing all three Pathway Tools components
(Navigator, Editors, and PathoLogic) should now be able to access
PGDBs stored in Oracle and MySQL, on the Sun/Solaris, Linux, and
Windows platforms. The Oracle-related bug that prevented reliable
access to PGDBs stored in Oracle by Pathway Tools version 9.5 has been
fixed by a new release of the Oracle InstantClient library.
- New ptools-local directory. In previous versions of Pathway
Tools, PGDBS created by users with PathoLogic were stored within the
aic-export directory structure that also contained the Pathway
Tools software. In version 10.0, the storage location for
user-created PGDBs changes to be within a new directory called
ptools-local that resides outside the aic-export
directory. The ptools-local directory is shared by all users
who share a given installation of Pathway Tools, and is retained when
new versions of Pathway Tools are installed later. The user specifies
the location of the ptools-local directory during the
installation process. It can reside anywhere, such as in the home
directory of one user of Pathway Tools, or in a more central location.
As well as containing PGDBs, ptools-local contains other user
data such as the new Pathway Tools initialization file.
- New Pathway Tools initialization file.
A new initialization file called ptools-local/ptools-init.dat
contains site-specific definitions of Pathway Tools parameters, and is
shared by all users who share a Pathway Tools installation. This file
must be manually configured by the installer of Pathway Tools.
- aic-export directory structure changed. The structure
of the aic-export directory structure containing Pathway
Tools has been altered in a number of ways.
- Auto-checkpointing of PGDB updates.
For PGDBs stored in a relational DBMS (but not for file PGDBs), Pathway Tools
now has an auto-checkpoint capability such that every 5 minutes it
automatically checkpoints to a file all PGDB updates that have been
made since the last DB save operation. Should the system crash,
those updates can be restored by opening the PGDB and executing
File→Restore Updates from Checkpoint File.
- New command-line arguments -eval and -load.
Pathway Tools recognizes two additional command-line arguments when invoked from Unix: -eval and -load.
The former evaluates a specified Lisp expression; the latter loads and evaluates all Lisp expressions
within a specified Lisp file.
- User preference defining RDBMS username.
A new user preference, under general preferences, allows the user to set the username that
will be recorded in save transactions for PGDBs stored in relational DBMSs. This
preference is useful when the same user has different computer accounts with
different user names, but wants all their save transactions to be recorded with
the same username.
- PTOOLS_RDBMS_LOGIN obsolete.
This environment variable was previously used to supply relational DBMS
login information to Pathway Tools, but is no longer used in favor of
two variables in the Pathway Tools initialization file: RDBMS-Username and RDBMS-Password.
Changes to the Pathway/Genome Navigator
- Extensions to Reactions → Find Rxn by Substrates.
This command has been extended to permit more versatile searching of
reactions by their substrates, such as searching for reactions based
on combinations of exact substrates, chemical substructures within
substrates, and substrate chemical classes.
- Compound windows link to regulated enzymes.
Compound display windows now list those enzymes that are activated or
inhibited by the compound, and those enzymes that require the
compound as a substrate.
- Gene and protein windows show sequence length.
Gene and protein sequence lengths are displayed in gene and protein
display windows, respectively.
Changes to the Pathway/Genome Editors
New duplicate frame command. This new command under the
right-click Edit menu allows the user to create a new reaction,
compound, or pathway by duplicating an existing object. After
duplication, the appropriate editor is brought up on the newly created
duplicate, so the curator can edit it right away.
Release Notes for Pathway Tools Software Version 9.5
Released on September 30, 2005.
General Changes
- New Interfaces to Oracle and MySQL: To facilitate
(1) concurrent multi-user editing,
(2) auditing of all edits, and
(3) faster data access,
we've added the option of storing user-created databases in an
Oracle 10 or MySQL 4 server. (We haven't tested with Oracle 9.)
Previously, Pathway Tools on the Solaris operating system came with an option
to use Oracle 8, which is now quite outdated.Now, each curator can run Pathway
Tools on their Solaris, Linux, or Windows computer without concern for which
operating system other curators of the same database are using,
assuming your database administrator installs Oracle or MySQL on a
different computer than those computers running Pathway Tools. For more
information, and for information on these RDBMS options, see URL
http://bioinformatics.ai.sri.com/ptools/installation-guide/released.
- Pathway Tools now uses a new ontology of cellular components to describe
cellular locations, such as protein locations, and locations of molecules
that are substrates of transport events. A web site describing this ontology
will be available shortly at URL
http://bioinformatics.ai.sri.com/CCO/.
- The pathways.dat flatfile now includes super-pathways.
Changes to the Pathway/Genome Navigator
- Enhancements to the Cellular Overview diagram:
- The Web version of the Overview Diagram (example)
now provides more interactivity: when a compound icon
in a pathway is clicked on, a magnified image of the pathway appears,
including all compound names and genes, as well as a menu offering a
choice of where to navigate to.
- Display of Omics data on individual pathways: In the web version of the Omics viewer,
Omics data is superimposed on magnified pathway diagrams within the
Overview, including showing different colors (data values) for different isozymes
where appropriate. There is also the option of generating a table of
individual pathway displays for all pathways whose Omics values exceed
a specified threshold. In the desktop version of the software,
navigating to an individual pathway page after uploading Omics data to
the Overview will show the data on that pathway.
- The web version of the Omics Viewer now offers a three-color
display option in addition to the previously available full color
spectrum. This capability was already available in the desktop
version of the software.
- The Omics Viewer now provides instructions for saving the
generated display (including animation and/or pathway popups) to your
local disk as an html file.
- New Comparative Analysis capabilities
- The Comparative Genome Browser can be used to examine several
replicons (chromosomes or plasmids) simultaneously side-by-side. This
allows easy visual comparison of related organisms to observe
similarities and differences in their gene arrangements. Orthologous
genes are shown in the same color across the organisms.
As an example, the trpA gene is aligned here
for 3 E. coli strains and one Shigella strain.
- NOTE: Ortholog information for all BioCyc DBs will be available
through the SRI Web site by October 2005. However, ortholog
information in the desktop (downloadable) BioCyc is only
available for several E. coli related DBs in version
9.5; later versions will contain expanded ortholog information.
- New Summary Tables
compare various attributes relating to reactions, pathways,
transcription units, etc. across a specified set of organisms.
Note that this functionality is available through the Web mode
of Pathway Tools only, that is, you must run Pathway Tools using
the -www option to access this functionality.
- The Cross-Species Comparison button in reaction and pathway displays
allows a particular reaction or pathway to be compared across a
selected list of organisms.
- The previously separate display pages for a polypeptide and its homomultimeric complex were
combined into a single page.
- The Web Query page now allows search by accession number or id
from any other database we link to. For example, typing P76078 (a
Swiss-Prot link) or EG13736 (an ecogene link) into the search box will
retrieve the protein or gene that has a unification link to that id
(exact match only).
- The Query Results web page now includes a description of what
kind of data appears in each type of web page. It also includes links
to transcription unit pages.
- Pathway Tools can now generate a Genbank file describing the
contents of a PGDB. Because Genbank format was not designed to capture
the full range of information within a PGDB, our Genbank file export
capability can only partially capture the contents of a PGDB. The
exporter can be invoked using the command
File→Export→Selected Chromosome to Genbank File...
- Improvements to the new genome browser:
- The extent of transcription units (operons) is now shown by a grey background color; in
addition, genes are colored to reflect membership in transcription units. Mousing
over the grey transcription unit region will produce a pop-up showing what transcription
factors control the expression of that transcription unit.
- To re-center the magnified region of the chromosome on a given gene,
click on a tick mark under that gene.
- The new command File→Summarize Current Organism
displays the organism summary page for the current organism.
- Added new command invoked by right-clicking on an object called
Show→Frame in all databases, and renamed right-click
Show→Frame in other species to Show→Frame in other
database.
- Base position in gene page is now displayed as
start arrow end where start is always the smaller base
position and arrow indicates the direction of transcription.
Examples:
- 300,001 → 300,901
- 200,001 <- 200,601
- In the desktop version, the information in all Database Links can be
shown by right-clicking. The creation-date of the link is also shown
now.
- Start codons are now denoted in FASTA sequence output in a
different case than the remainder of the sequence.
- Transcription unit figures now show promoters and binding sites
with low quality evidence using a dashed outline (as opposed to a
solid outline for those with high quality evidence).
Changes to the Pathway/Genome Editors
- New Marvin chemical structure editor: The Marvin molecular
structure editor Java applet has been integrated with Pathway Tools
for use as a chemical structure editor. Users now have a choice of
using either Marvin or the JME editor. Relative advantages of these
two tools are that JME is very simple to use, but Marvin is much more
feature-rich. Marvin can be used for entering compound structures
with atoms called R, R1, R2, etc., by using the atom-alias feature.
For more information see page 81 of the Pathway Tools User's Guide
vol.II. Also, it is now possible to clear and completely delete a
chemical structure in a PGDB, using Marvin or JME.
- Users can now enter hyperlinks to other PGDB objects within the
comment text for any object, allowing clickable references to other
PGDB objects to be embedded within comment text.
- To remove an association between an enzyme and a reaction it
catalyzes, right click the protein and, in the menu that pops up,
select: Edit→Remove Reaction
- To merge two reactions into a single frame, right-click on one
of the reactions and select: Edit→Merge Reactions
Changes to PathoLogic
- Inference of Transport Reactions: PathoLogic contains a
new inference module called the Transporter Identification Parser
that infers transport reactions within a PGDB from
free-text descriptions of transporter function. Inference of transport
reactions is valuable because transport reactions allow Pathway Tools to compute
with the functions of transporters, such as to add transporters to the
Cellular Overview diagram automatically.
Developed in collaboration with Dr. Ian Paulsen of TIGR, this program
performs a textual analysis of the English descriptions of protein
function within a PGDB stored within the Common-Name field of each
protein. It determines which proteins are transporters, what is the
transported substrate and the direction of transport, and what energy
coupling mechanism is employed by the transporter. When the program
is able to identify all of these fields it creates a reaction object
within the PGDB that precisely describes the transport event that the
transporter achieves. An example reaction for an ABC transporter for
L-lysine for a Gram-negative bacterium is:
L-lysine [periplasm] + ATP = L-lysine [cytoplasm] + ADP + Pi
That is, the transporter moves L-lysine from the periplasm to the
cytoplasm in conjunction with hydrolysis of ATP.
A user interface permits review and editing of individual transport reactions.
- PathoLogic is now supported on Windows 2000 and Windows XP. Now,
essentially all of Pathway Tools runs on three operating systems:
Linux, Solaris, and Windows. NOTE: Due to factors (bugs) beyond our control,
release of the Windows version of the full Pathway Tools including PathoLogic
will be delayed; we will make an announcement when this build is available
thorough our download site.
- PathoLogic now properly recognizes and processes pseudogenes. PGDB objects are created
for pseudogenes, but no objects are created for the gene products since no gene products are produced.
See the manual for details on how to specify pseudogenes in the input files.
- PathoLogic can now use other organism PGDBs as additional
references for pathway prediction. For example, if you have
curated new pathways into a PGDB you have created, and you wish
to create a second PGDB, you can tell PathoLogic to consider
pathways in both MetaCyc and in your first PGDB for possible
prediction in the second PGDB.
Release Notes for Pathway Tools Software Version 9.0
Released on February 22, 2005.
General Changes
- The Microsoft Windows version of Pathway Tools is easier to install.
- The Microsoft Windows version of Pathway Tools is now easier to run as a web server.
Third-party Mozilla plug-in BioBar can search several bioinformatics web sites, including BioCyc.
Changes to the Pathway/Genome Navigator
- New Genome Browser:
Chromosomes and plasmids can be examined in a new horizontal
genome browser. For example, see the browser centered around gene
dnaA.
Some of the key features are:
- At the top of the page, the full length of the chromosome is shown at low
resolution. A selected region of the chromosome is displayed
at higher magnification in the lower part of the screen.
- The full chromosome view at the very top indicates the magnified
region by means of a red, rectangular cursor.
- Magnified regions can be wrapped over several lines, thus showing
more context.
- Several levels of semantic zooming show increasing detail upon
increased magnification.
- Protein ORFs are visually distinguished from RNA genes, and
when genes belong to the same operon, they are assigned the same color.
- An improved navigation interface offers a panel of control arrows that
allow translation and zooming. Additionally, base-pair positions or a
gene name can be manually entered into text entry boxes to position the
browser.
- Mouse-over of genes shows gene names and intergenic distances
to the neighbors in base-pairs. Mouse-over of promoters shows the activating and
inhibiting transcription factors.
- Improved operon depiction in gene pages: The transcription unit diagram at the bottom of gene pages has been
modified to show more of the genome context around a given gene -- it shows
the entire operon of the gene, and surrounding genes. Additional
diagrams showing all of the gene's transcripts are now
generated, and are aligned to the first diagram. For example, see the display for gene dnaA
- More compact pathway diagrams: The pathway-drawing capabilities have been improved so as to produce more compact diagrams in many cases. For example, see this pathway.
Changes to PathoLogic
- Pathway Hole Filler:
In the "Candidates to Fill Pathway Hole" page, which displays for each candidate a summary of the evidence used to evaluate
the candidate, we have replaced the lists of reactions associated with the candidate and the pathway hole with a Gene-Reaction Schematic for each. The Gene-Reaction Schematic for the candidate displays the candidate and its associated reactions in the user's KB. The schematic for the pathway hole displays the missing reaction and its associated reactions and genes in MetaCyc. A comparison of these two schematics will assist the user in deciding which candidate(s) to assign to each pathway hole.
Release Notes for Pathway Tools Software Version 8.5
Released on September 17, 2004.
General Changes
- Pathway Tools and BioCyc licensing, which formerly required a paper license agreement, are now processed entirely online at
http://BioCyc.org/download.shtml.
- Cellular Overview and Omics Viewer Improved:
The Cellular Overview diagram within Pathway Tools has been
improved in many respects, and the Expression Viewer has been renamed the Omics Viewer to reflect its expanded functionality. See
for example the
E. coli Omics Viewer.
Improvements include:
- Users can create combined displays of gene expression, proteomics,
metabolomics, and reaction flux measurements on the Omics Viewer
- Drawing speed is improved
- Metabolic pathways in the Overview are now grouped by pathway class,
with additional information shown on mouse-over
- Zooming of the diagram is supported (desktop version only)
- The periplasm and outer membrane have been added to the diagram,
as have those proteins present in the periplasm and outer membrane
- The layout of the Cellular Overview can be computed completely automatically
by PathoLogic in a new PGDB, obviating the need for users to manually
lay out the diagram
- Compound Stereochemistry: Pathway Tools now supports
stereochemistry for chemical structures in its schema and in its display
of chemical structures. Many chemical compounds in our PGDBs
now contain stereochemical information in their structures.
Editing of chemical structures is now
supported via the JME chemical editor.
- JME Chemical Editor Now Supported: Pathway Tools
now provides an interface to the JME chemical editor. JME
was written by Peter Ertl of Novartis. It supports editing
of stereochemistry, and is generally superior to the
native chemical editor provided by Pathway Tools, therefore
SRI now encourages the use of JME instead of the old editor. JME is not included in
the Pathway Tools distribution, but may be obtained from
Novartis. It is freely available for academic users -- see
http://www.molinspiration.com/jme/doc/index.html. Instructions
on how to install it for Pathway Tools are in Section 2.3.8 of
the Pathway Tools User Manual, Volume II.
- Import/Export from/to Molfiles: Chemical structures
can now be imported from and exported to the molfile format.
This functionality is available under the Edit menu when
the user right-clicks on a compound.
To use this feature, right click the title of a compound display, and select one of:
Edit > Import compound structure from molfile...
Edit > Export compound structure to molfile...
Changes to the Pathway/Genome Navigator
Please note that some changes apply to the Web version of the
Navigator, some apply to the desktop (locally installed) version, and
some apply to both versions.
- Ontology Viewer Improved (web version): Web pages
depicting ontology class hierarchies now use an improved
hierarchy browser. See for example the
MetaCyc pathway ontology.
- Web Pages Listing Compounds, Enzymes, and Genes:
The Web Query Form now allows
the user to generate alphabetical listings of all pathways, proteins, genes,
and chemical compounds for the selected PGDB, in the third main bullet
in this page.
- Species Abbreviations in MetaCyc Pages: In MetaCyc
display pages for reactions, pathways, etc, it can be difficult to
tell the source species for a given enzyme or gene. Therefore,
MetaCyc display pages now include a two-letter species code in gene
and enzyme names consisting of the first letter from the genus and
species name. For example, the enzyme phosphoglycerate kinase and its
gene pgk from Pseudomonas aeruginosa would be depicted as
phosphoglycerate kinase (Pa) and Pa-pgk, respectively.
- Changes to Gene-Regulation Schematic: The gene-regulation
schematic diagram in pathway pages summarizes genetic regulatory
relationships for all genes in a pathway. The node and edge shapes
in the diagram have been updated to use more standard conventions
for depicting activation, inhibition, and dual regulation.
Changes to PathoLogic
- Pathway Hole Filler: The user interface for the third step of
the Pathway Hole Filler (Choose Candidate Holes to Fill in KB) has
been completely overhauled to make the process more straightforward and
efficient. In the new version, the interface provides the opportunity
to review the evidence for all candidates identified for each pathway
hole. The first page displays for each pathway hole the top scoring
hit above a cutoff determined by the user. From this page, the user
may access another window (Candidates to Fill Pathway Hole) which
displays for each candidate a summary of the evidence used to evaluate
the candidate. This page also includes other data available in the KB
for the candidate (e.g., other reactions catalyzed by the candidate)
and the pathway hole (e.g., all pathways where the reaction is
missing). The process of manually reviewing each candidate and choosing
which holes to fill has been drastically streamlined by
gathering all the relevant information into one page.
- PathoLogic Accepts NCBI Taxonomy ID: Users can
supply the NCBI Taxonomy ID of the organism to which
PathoLogic is being applied in the database-creation
dialog to facilitate linking of the PGDB to the NCBI Taxonomy
database.
Release Notes for Pathway Tools Software Version 8.0
Released on March 12, 2004.
General Changes
- Napster Comes to Bioinformatics: A peer-to-peer sharing mechanism for
Pathway/Genome Databases (PGDBs) has been implemented for Pathway Tools. This
mechanism consists of a registry server running at SRI that maintains
a list of PGDBs that have been registered for sharing. You can use the
Pathway Tools program to register PGDBs that you have created for sharing
(they are deposited on your own FTP site for downloading by others),
and to download PGDBs listed on the registry. You can view the
current contents of the Registry on the Web at URL
http://biocyc.org/registry.html, or
from Pathway Tools 8.0 with the command: Tools→Browse Downloadable PGDBs. We encourage you to
register PGDBs that you have created, using the command Tools→Publish PGDBs.
For more information, see the Pathway Tools User's Guide.
- Pathway Hole Filler: Metabolic pathways that were computationally
predicted by PathoLogic often contain reactions that have no
identified enzymes within the genome. We call those reactions pathway
holes. A new Pathway Tools prediction algorithm that you can run on
an existing PGDB predicts which genes within the genome code for
enzymes that fill these holes. When applied to a microbial genome, it
can generate 50-100 new gene function identifications. A manuscript
describing this algorithm
is available here. For more
information, see the Pathway Tools User's Guide.
- Protein Features: Pathway Tools now supports editing and display
of protein features. The protein editor allows users to define many
different types of protein features on a protein, such as metal binding
sites, disulfide bond locations, chemically modified residues, homology domains, repeats, signal sequences,
DNA binding regions, and transmembrane regions. To add a new feature to
a protein, right-click on the name of the protein in a Navigator display,
and select Edit→Add Feature. Features are displayed schematically in
Navigator protein display windows.
- Oracle passwords: For users who have stored newly created PGDBs
within an Oracle server, Pathway Tools no longer requires a
fixed Oracle login and password. The following pertains to
the Unix environment variable PTOOLS_ORACLE_LOGIN:
If the environment variable is:
- Set to "PROMPT", the software will prompt the user for login/passwd
- Set to anything else, the software use that value as login/passwd
- Unset, the software will use the previous hard-coded value
Changes to the Pathway/Genome Navigator
Please note that some changes apply to the Web version of the
Navigator, some apply to the desktop (locally installed) version, and
some apply to both versions.
- Navigator main menu redesigned: (Desktop version) The main
menu of the desktop version of the Navigator has been completely
redesigned. Rather than having query modes such as "Compound Mode,"
queries are now accessed from a menu-bar whose items include
"Compound," "Pathway," etc. This approach is more familiar to most
users, and frees up screen real estate.
- Protein display windows redesigned: (Web and desktop) The
protein display windows have been redesigned in several respects. The
polypeptide display window now displays information about a complex
that contains it, much as a complex window contains information about
its subunits. The styling of subunit composition has been re-worked
somewhat. And in displays of transcription factors, information about
all modified forms of the transcription factor are shown on one page.
- New queries: (Desktop) The following new queries have been implemented:
- New RNA navigation features include Get RNA by name, Get RNA by Substring,
Get RNA by Class.
- Retrieve arbitrary DNA sequences: (Web) We have added the ability to retrieve or zoom to arbitrary DNA sequence regions from
gene pages. Click on the button "Nucleotide Sequence Neighborhood"
near the top of each gene page.
- Small map updated: (Web and desktop) The small genome map displayed below a pathway drawing has been
improved to print more meaningful information when the user
moves the mouse over the tick marks that represent genes within
the pathway.
- New Overview metabolite shape: (Web and desktop) We have
added a new compound shape to the Overview diagram: upside-down
triangles represent cofactors.
Changes to the Pathway/Genome Editors
- The reaction editor now supports fractional coefficients.
- Several bugs in the Create/Add Protein dialogs have been fixed.
- The compound structure editor has been modified to use a horizontal menu bar
instead of the older vertical menu.
- The reaction balance checker has been modified to tell the user that
it does not try to balance hydrogens due to the complications with
respect to portraying compounds in their correct ionization states,
for example, different compounds in our databases are stored in
different somewhat inconsistent ionization states, making
balancing of reactions with respect to hydrogens very difficult.
Changes to the PathoLogic
- New batch mode: PathoLogic can now operate in batch mode,
meaning that it can automatically create PGDBs for one or more
organisms based on invocation from the Unix command line. The
command-line invocation specifies a directory that PathoLogic should
examine to find input files, such as one or more Genbank files for the
PGDB to create. The fact that this processing is completely automated
means that the resulting PGDBs lack elements that are created
manually, such as an Overview diagram. For more information, see page
1-38 of the Pathway Tools User's Guide, Volume II.
Release Notes for Pathway Tools Software Version 7.5
Released on August 29, 2003.
General Changes
- A general import/export facility for frames has been added. Sets
of frames can be exported to and imported from character-delimited
files, which can be imported into a spreadsheet program, edited, and
re-imported. Frames can also be exported to an attribute-value format
similar to MEDLINE format, and re-imported into a different KB.
- The bug report form has been changed to make it easier to
use.
- It is now possible to install Pathway Tools with any of the
buttons on the main query page (help, pathway tools home, etc.)
redirected to a custom user-specified URL.
- An ontology of evidence codes has been added to the Pathway Tools schema,
in order to capture the evidence (computational, experimental, type of
experiment, etc.) for the existence of various entities (pathways,
protein functions, transcription units, etc.) in an organism.
Pathway Tools has been extended so that the pathway and operon predictors
within PathoLogic decorate the pathway and operon PGDB objects that
they create with evidence-code information, indicating computationally
predicted objects as such. The Editors have been extended to include
functionality that allows users to interactively enter and modify
evidence codes within PGDB objects. The Navigator has also been extended to
display evidence information.
Changes to the Pathway/Genome Navigator
- Desktop mode (not Web mode): Several new types of queries have been added:
- Query pathways by reactants and products.
- Query proteins by molecular weight and pI.
- Query compounds by conjunctions of name, molecular weight, chemical
formula, and substructure properties.
- The bottom of each Pathway Tools object display page now shows the
full reference list for all references cited in that page. In desktop mode,
a new preference under the Preferences menu allows the user to influence
how citations are displayed (e.g., "[1]" vs "[Smith85]").
- Displays of the parent classes of an instance have been reworked to
be more intuitive; they now show the complete class inheritance path back
to the roots of the class hierarchy.
- Web mode: A new "All" query is available, allowing users to query all
object types by substring with one query. The matching objects are
grouped by object type (pathways, proteins, etc).
- The list of reactions in the compound display is sorted according
to the role that the compound plays in each reaction.
- MetaCyc's pathway displays now has an option to show all enzymes
for reactions, even for organisms that do not have the pathway.
- Display of chemical structures has been improved.
Changes to the Pathway/Genome Editors
- There is now an editor for RNAs, which also allows the creation
of RNAs for genes.
- The compound structure editor now allows charges to be entered
along with each atom.
Release Notes for Pathway Tools Software Version 7.0
Released on February 28, 2003.
General Changes
- The set of flat-file dumps has been expanded somewhat to contain
some additional files, and additional fields per file. Comments and
citations are now included in the flat files, and there is a new
Publications flat file.
- Pathway Tools now supports introns, exons, and alternative splice forms in its
display and editing tools.
Changes to the Pathway/Genome Navigator
- Consider the display of a MetaCyc pathway for which data from multiple enzymes
from different species is available. Initially the pathway display
shows all enzymes, but you can use a menu at the top of the pathway
page to generate a species-specific views that shows only the enzymes
from that species.
- The expression viewer can now load expression data in the format
used by the SAM program for Significance Analysis of Microarrays
(see URL http://www-stat.stanford.edu/~tibs/SAM/)
- Desktop mode (not WWW mode): Right-clicking on a database link
allows you to request additional information about that link.
- Desktop mode: The Overview scaling size preference is now
properly saved across sessions.
- WWW mode: You can now query multiple objects by name or
identifier simultaneously in the Pathway Tools query form, by
entering their names or identifiers, separated by commas
- Chemical Abstracts registry numbers are now implemented in all DBs
as database links, rather than as a field in the schema.
- You can view the user guide using a command under the Pathway
Tools help menu "Show User Guide"
- WWW mode: The Pathway Tools WWW server now attempts to detect
and block web crawlers
- It is possible to run a Pathway Tools WWW server in a mode whereby
it suppresses display of gene pages for an organism by generating
URL links to another genome database for the organism. This mode
allows an existing genome database to interoperate closely with a
pathway database for the organism managed by Pathway Tools.
See the section on invoking Pathway Tools in the User's Guide for
more information.
Changes to the Pathway/Genome Editors
- The chemical compound structure editor has been documented
in the User's Guide, and the tool been overhauled and extended. This tool can be used to enter or modify
small-molecule structures.
- The pathway editor now allows the user to add/delete arrow links between
pathways, and to mark reaction steps as hypothetical.
Changes to PathoLogic
- A new command under the PathoLogic Organism menu allows the user to create a copy of an entire
Pathway/Genome Database.
Release Notes for Pathway Tools Software Version 6.5
Released on August 30, 2002.
Changes to the Pathway/Genome Navigator
- The viewer for painting expression data on the full metabolic
overview has been expanded to support animated display of multiple
expression time-points, and to
allow the user to specify the
colors used for different ranges of expression values. Several
bugs have been fixed in the expression viewer, performance has
been improved, and better detection of malformed input files
has been added.
- In previous versions of the Navigator, the WWW server capability
that allowed the Navigator to publish Pathway/Genome Databases on the
WWW ran only on the Sun. Now that capability runs on the PC/Windows
platform as well.
- A Perl API called PerlCyc now exists to allow Perl programmers to
query Pathway/Genome Databases. See the documentation for the
Pathway Tools command-line argument "-api".
- We have expanded the set of flatfiles generated for Pathway/Genome
Databases. Click Here
for descriptions of the flatfiles.
Changes to the Pathway/Genome Editors
- The Editors can now export a pathway to a file, and import pathway
from an exported file. See commands under Special→Misc.
- A publication editor has been added for defining new references
in a PGDB.
Changes to PathoLogic
- A new command under the PathoLogic Organism menu allows the user to create a copy of an entire
Pathway/Genome Database.
Release Notes for Pathway Tools Software Version 6.0
Released on February 25, 2002.
Changes to the Pathway/Genome Navigator
- The Navigator has been ported to Windows-98 and higher versions of Windows.
- A new facility called Auto-Patch allows you to easily
download software patches from the SRI website.
The command Special → Misc → Install Patches → Download
patches from the Web, will automatically download new software
patches from the SRI Web site and load them into your running program.
Auto-patch downloads will also occur whenever you install the software.
- A HELP button has been implemented for the Gene-Reaction Schematic,
and for the Gene-Regulation Schematic.
- The Organism Summary Page for a given Pathway/Genome DB now includes a
listing of the authors and their institutions, and a list of
citations, for that DB.
- The local Navigator now allows retrieval of an arbitrary
nucleic-acid sequence region (see Show Sequence command under Gene Map
Mode).
- A new command-line option allows the user to specify the default
organism to which queries will be directed within the Navigator
in Web mode.
- Many bug fixes and performance improvements have been made to
the Navigator, particularly to the gene-expression pathway viewer.
Changes to PathoLogic
- The documentation for PathoLogic and for the Pathway/Genome Editors
has been completely overhauled.
- The PathoLogic graphical user interface has been completely rewritten
to facilitate creation of new Pathway/Genome Databases.
- A new PathoLogic interface accessible through the command
Refine → Assign Probable Enzymes assists the users in
manually assigning biochemical functions to gene products.
- The PathoLogic pathway evidence report has been improved significantly.
- The Pathway Tools has been upgraded to work in conjunction with
Oracle 8i instead of version 7 of Oracle.
Release Notes for Pathway Tools Software Version 5.4
Released on February 10, 2001.
Changes to the Pathway/Genome Navigator
- The hostname in EcoCyc and MetaCyc URLs has changed from
ecocyc.PangeaSystems.com to ecocyc.DoubleTwist.com.
- The ability to paint expression data onto the Overview is now
available through the WWW. From the query page at
http://ecocyc.DoubleTwist.com:1555/server.html,
in the first line under "Links to summary information about the selected organism," click
on "Expression viewer."
- The Overview visualization now depicts the
cytoplasmic membrane and its transporters,
for those transporters defined as database objects.
- The Navigator now produces displays of the transcription unit that contains a given
gene, and of all transcription units controlled by a given transcription factor.
- The gene window now allows the user to retrieve both the
nucleotide sequence of the gene, and the amino-acid sequence of the
gene product.
- The chromosome viewer now contains active arrow keys for moving
a child map up and down, and for changing the magnification of a
child map. The viewer also now depicts promoters at high levels of
magnification.
- The Highlight command within Overview mode now includes an option
for highlighting reactions according to the cellular locations of the
enzymes that catalyze a reaction.
- We have upgraded the look-and-feel of the WWW Navigator.
Release Notes for Pathway Tools Version 5.0
Released on June 1, 1999.
Changes to the Pathway/Genome Editing Tools
Many minor improvements were made to the Editing Tools in this release to
increase their reliability.
- The behavior of the right-click menu Edit→Create-And-Edit-Frame has
been modified to allow the user to specify the class of the new instance.
- The GKB Frame Editor now suppresses display of many slots that
most users will not be concerned with. These slots can be displayed using
a selector in the Frame Editor Preferences dialog.
- The Revert and Refresh KB operations now redisplay current
Pathway Tools windows in case those operations altered the currently displayed
objects.
- The Special→KB menu has been reorganized.
- When an asterisk ("*") is printed next to the name of an organism (such as in
the organism-selector menu or in the window title line) it means that unsaved
KB changes exist for that organism.
Changes to the Pathway/Genome Predictor (PathoLogic)
- PathoLogic now uses the MetaCyc database as its reference pathway
database, thus significantly increasing the range of pathways it can
predict for an organism.
- PathoLogic now properly copies its HTML summary reports into a directory that is
accessible by the Pathway Tools in WWW mode.
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