Releases | Open Source Science

psamm - PSAMM 1.2.1

fix bug in generate-database
revise formatting of doc

- Python
Published by yingzhanguri almost 4 years ago

psamm - PSAMM 1.2

Adds the new psamm-generate-model command with the options of generate-database, generate-transporters, and generate-biomass, which construct metabolic models in the KEGG namespace
Adds the new option translated-reactions to the tableexport command
Added translated reactions to excelexport
Fixed compatibility in documentation for Gurobi for python versions 3.7
Adds support for Python 3.8 and 3.9

- Python
Published by yingzhanguri almost 4 years ago

psamm - PSAMM 1.1.2

Drops support for Python 2.7 (deprecated Jan. 01, 2020), 3.3, and 3.4
Adds the --phin and --phout options to the tmfa command
Adds descriptive counts of the number of reactions and compounds curated in the manual curation option of modelmapping

- Python
Published by esameth almost 5 years ago

psamm - PSAMM 1.1.1

Fix bug where the psamm modelmapping translate_id command requires the undefined parameter --dest-model

- Python
Published by esameth about 5 years ago

psamm - PSAMM 1.1

Adds the new vis command for visualizing metabolic pathways and networks
Adds the new tmfa command to implement the approach as described in Henry et al., 2007 (PMID: 17172310) and Hamilton et al., 2013 (PMID: 23870272).
Performance updates to the model-mapping command
Updates to export full models from gimme and psammotate
Added the --fva option to the robustness command

- Python
Published by esameth about 5 years ago

psamm - PSAMM 1.0

Adds the new modelmapping command for mapping reactions and compounds ids between different GEMs.
Adds the new psammotate command for generating draft GEMs using a template model and a mapping of orthologous genes to another organism.
Adds the new gimme command which implements the GIMME algorithm as described in Becker and Palsson, 2008 (PMID: 18483554).
Updates the search command to allow for searching of strings within any reaction or compound property.
Updates to the tableexport and excelexport commands to allow for the export of additional gene and reaction information.
Adds new section to the tutorial to detail how to use the findprimarypairs commands.
Renamed duplicatescheck command to dupcheck.

- Python
Published by yingzhanguri about 6 years ago

psamm - PSAMM 0.31

The psamm-import tool has been moved from the psamm-import package to the main PSAMM package. This means that to import SBML files the psamm-import package is no longer needed. To use the model-specific Excel importers, the psamm-import package is still needed. With this release of PSAMM, the psamm-import package should be updated to at least 0.16.
The tutorial was updated with additional sections on using gap-filling procedures on models.

- Python
Published by yingzhanguri over 8 years ago

psamm - PSAMM 0.30

Adds the new command primarypairs for predicting reactant/product element transfers using the new FindPrimaryPairs method as well as the MapMaker method.
A new option has been added to the genedelete command which allows use of minimization of metabolic adjustments to simulate biomass production for gene knockouts.
Fixes a bug where the epsilon parameter was accidentally ignored by fastgapfill.
Fixes a bug where the psamm-sbml-model command did not ignore boundary species. With this change, the boundary species are also ignored by default when using the API to read SBML models.
Fixes a performance issues with gap-filling that made the gapfill and fastgapfill commands take much longer time to run on large models than necessary.

- Python
Published by jonls over 8 years ago

psamm - PSAMM 0.29

The tutorial in the PSAMM documentation has been updated and expanded to include additional information on using PSAMM for model curation and constraint-based analyses.
The experimental command psamm-sbml-model was added which makes it possible to run any command from psamm-model (e.g. fba, robustness, etc.) directly on an SBML file. For now this only supports SBML level 3 files with FBC. This provides a quick way of running basic analyses on SBML files. We still recommend importing the SBML file to YAML format with psamm-import for anyone wishing to make changes to a model.
Fixes access to charge parameter parsed from SBML files. The charge is now correctly imported with psamm-import.
Fixes import of compartments from SBML files. The empty boundary compartments are now no longer included in the import.
Fixes bug in writing the reaction flux limits sheet of the excelexport command.
The console command was changed to only provide the model variable since the metabolic model can easily be created.

- Python
Published by jonls almost 9 years ago

psamm - PSAMM 0.28

The YAML model format now allows users to specify compartment information and compartment boundaries in the model.yaml file. See the file format documentation for more information.
The media key in the model.yaml has changed name to exchange to reflect the fact that not only uptake exchange must be defined here. The media key is still supported but has been deprecated.
The gap-filling command gapfill and fastgapfill now use the compartment information to determine which artificial transport and exchange reactions to add. This means that a model must specify compartments and compartment boundaries when using gap-filling commands.
The gapcheck command now has two new methods for detecting blocked compounds. The new prodcheck is a more robust version of the GapFind check which was previously used. The new sinkcheck method will find compounds that cannot be produced in excess. This can find some additional blocked compounds that were not detected by the other methods.
The gapcheck command now reports blocked compounds in the extracellular space. Previously, these compounds were excluded. An option is available to switch back the old behavior of excluding these from the final output.
The gapcheck command now has an option to run the check with unrestricted exchange reactions.
The gapfill command can now be run without implicit sinks. This makes it possible to use this command to solve additional model gaps. It is still recommended to first solve gaps using implicit sinks, then later disable implicit sinks when all other gaps have been closed.
The gapfill command now has an option to enable the bounds expansion proposals (e.g. making irreversible reactions reversible). By default this option is now off.
The fastgapfill has improved output that contains less superfluous information. The output format is now identical to the gapfill command. The fastgapfill also no longer runs an FBA on the induced model since this caused some confusion.
Added new command checkduplicates which detects whether the model has multiple reactions with the same (or similar) reaction equation.
The sbmlexport command now allows the user to specify a file path. The command can also optionally output the SBML file in a more readable format with an option.
Fixed support for the latest CPLEX release 12.7. A change in their API made PSAMM incompatible with the 12.7 release. This is now fixed.
We now officially support Python 3.5 and Python 3.6.

- Python
Published by jonls about 9 years ago

psamm - PSAMM 0.27

When exporting a model with excelexport, sbmlexport or tableexport, the current Git commit ID of the model is now part of the export.
The gapfill command has been split into two separate commands. The new command gapcheck only reports which compounds are blocked without trying to fill gaps. The gapfill command now only reports the suggested reactions for gap-filling.
The tableexport command has been made more robust when the model properties contain special characters or structured data. Strings containing tabs or newline characters are now quoted in the output.
Improved error messages for multiple commands when reactions with forced flux (e.g. ATP maintenance reactions) impose impossible constraints.

- Python
Published by jonls about 9 years ago

psamm - PSAMM 0.26

All commands that perform loop removal now use the option --loop-removal to set the type of loop removal. The --tfba option is no longer available for the fva, fluxcheck and randomsparse commands, instead --loop-removal=tfba should be used.
All simulation commands that perform a maximization of an objective now take an --objective option that can be used to override the biomass reaction set in the model. The commands fba and fva no longer allow positional arguments to set the objective, instead the --objective option should be used.
All user data in the model is now exported with the sbmlexport command. User data that cannot be translated into a standard machine-readable SBML form will instead be stored in the SBML notes section.
The output from the gapfill command now shows the complete induced model (like fastgapfill) and also lists the compound IDs of the blocked compounds.
The gapfill command will now propose the removal of flux bounds if such a modification can unblock the model.
The gapfill command now excludes the biomass reaction from being modified in the induced model. Previously the biomass reaction was sometimes reversed in the induced model but this is usually not a desired solution.
The gapfill command now allows the user to specify penalties on added or modified reactions (like fastgapfill).
The gapfill command was changed so the --epsilon option now specifies the threshold for non-zero reaction fluxes (like the --epsilon in other PSAMM commands).
The gapfill command was changed to be more robust when handling small epsilon values. It will now lower the solver thresholds if necessary and will generate a warning when epsilon is too low. This fixes an issue where gapfill would previously fail or generate incorrect results with some models.
Fixed: The --exclude option in the formulacheck command did not work correctly.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.25

Fixed an error parsing decimal values in reactions which resulted in a failure to run FBA and other analyses on certain models.
The fastgapfill command no longer tries to unblock exchange reactions by default. Only internal reactions will be unblocked by default.
The fastgapfill command has a new --subset option to explicitly specify set of reactions to unblock. This means that the command can now be used to unblock a specific reaction.
The weight options on fastgapfill have changed name to --db-penalty, --tp-penalty and --ex-penalty for consistency with the existing --penalty option.
Fixed an error in gapfill that in some cases would result in a compound incorrectly marked as non-blocked.
The sbmlexport command now follows the FBCv2 specification for writing flux bounds, biomass reaction, gene products and various other properties to SBML files.
The sbmlexport command now uses the same ID for compartment IDs as used in the YAML files.
The order of compounds in the output from commands now reflects the order of compounds in the reactions as specified in the model files.
Experimental support for solving MILP problems with GLPK has been activated.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.24

When specifying flux bounds in media and limits, the fixed key can now be used when lower and upper limits are the same.
New column in output of excelexport and tableexport commands to indicate if reactions and compounds are in the model.
Zero mass compounds are now omitted from the output of the massconsistency command.
When exporting SBML file using the sbmlexport command, the exported compounds and reactions now have IDs that are based on the YAML model IDs. Characters that are not allowed in SBML IDs are transformed in a way that is compatible with COBRA.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.23

Fix a bug where no output of the randomsparse command was produced.
Make Cplex interface in PSAMM compatible with earlier versions (12.6 and 12.6.1) again.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.22

Better unicode handling in commands.
When running the gapfill command the epsilon parameter can now be specified on the command line.
When parsing reaction and compound entities from the YAML files, produce better error messages when IDs are invalid.
Work around a bug in Cplex that in rare causes a segmentation fault when a linear programming problem is solved repeatedly.
API: Add fastgapfill module which allows access to run the fastGapFill algorithm.
API: Add randomsparse module which allows access to generate a random minimal model which satisfies the flux threshold of the objective reaction.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.21

Add genedelete command to allow users to delete one or more genes and perform a viability check on the model after all related reactions are deleted.
Add balancecheck module which allows API access to charge balance and formula balance checks.
When a compound in the extracellular space doesn't have an exchange reaction, a warning would be provided so that the user may add the compound to the medium.
If a compartment is not given for a medium, it will now be assumed to have the extracellular compartment.
When using Gurobi and Cplex, the default optimality tolerance and feasibility tolerance has been decreased to 1e-9.
Fixed a bug where the reaction IDs are not printed properly in the result of chargecheck command.

- Python
Published by jonls over 9 years ago

psamm - PSAMM 0.20

Added experimental support for GLPK solver. MILP problems are not yet supported with this solver. GLPK also appears to have some issues with fastgapfill.
The gapfill command can now take a list of compounds on the command line that it will try to unblock. If a list of compounds is given, the command will not run GapFind but instead only use those compounds.
Remove the assumption that the extracellular compartment is always called e. The user can now specify the name of the extracellular compartment with the option extracellular in model.yaml.
In a previous release, the code interfacing with Cplex was updated and is now using an interface in Cplex that was introduced in version 12.6.2. The documentation now makes it clear that at least version 12.6.2 is required.
Update YAML format documentation on the model definition table format.
Work around issue with pkg_resources that resulted in import errors when running from IPython.

- Python
Published by jonls almost 10 years ago

psamm - PSAMM 0.19

When using Gurobi, the option --solver threads=X can now be used to specify the maximum number of threads that Gurobi can use.
The log messages from external libraries are more clearly marked as such. In particular, there should now be less confusion about the origin of the log messages from Cplex.
Internally, the LP solvers now support quadratic objectives. This will be used for various commands in the future.
Fix an error where an empty reaction would internally be detected as an exchange reaction.
Fix a bug where the compounds in the extracellular compartment were not correctly detected by gapfill.
Update documentation with information on how to cite the PSAMM publication.

- Python
Published by jonls about 10 years ago

psamm - PSAMM 0.18

Several commands now support parallelization with the --parallel option (fva, fluxcheck, fluxcoupling, robustness).
A more robust reaction parser is now used to parse reaction equations in YAML files. This also means that quoting compound names with pipes (|) is now optional.

- Python
Published by jonls about 10 years ago

psamm - PSAMM 0.17

When loading native models, PSAMM now uses the PyYAML safe loader and also uses the optimized CSafeLoader if present. This speeds up the start time of commands.
Various additional optimizations to model loading have been added. This speeds up the start time of some commands.
The fba command now shows the genes associated with each reaction for a quick overview of which genes influence the flux solution.
The sbmlexport command now properly exports gene association information.
All commands better handle output that contains unicode characters. In previous versions this would often fail when using Python 2.

- Python
Published by jonls about 10 years ago