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Recent Releases of metaboverse

metaboverse - Metaboverse-v0.11.6

What's Changed

Enhancements

  • Improved handling of global paths and variables
  • Added more robust build script for Windows
  • Updated metabolite mapping to better handle redox pairs (#171)
  • Added build helpers for devs

Bug Fixes

  • Fixed protein component edge color in visualization
  • Fixed path handling of modules and dependency files

Maintenance

  • Updated citation record DOI
  • Added tests for metabolite mapping
  • Implemented safer handling of relative paths for imports
  • Removed deprecated hmdb_mapper attribute

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.11.5...v0.11.6

- JavaScript
Published by j-berg about 1 year ago

metaboverse - v0.11.5

- JavaScript
Published by github-actions[bot] over 1 year ago

metaboverse - Metaboverse-v0.11.4

  • Add build workflows (https://github.com/Metaboverse/Metaboverse/issues/164)
  • Flexible file reading in case of bytes characters in user's input (https://github.com/Metaboverse/Metaboverse/issues/159)
  • Update toggle switches for clarity (https://github.com/Metaboverse/Metaboverse/issues/163)

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.11.3...v0.11.4

- JavaScript
Published by github-actions[bot] about 2 years ago

metaboverse - Metaboverse-v0.11.3

Addresses: - Fixes issues accessing pre-built files on Sourceforge and changing to Reactome database file keys (issue #159) - Removes unnecessary warning on app load/exit (issue #160) - And other minor formatting and stability changes

Note: I am having issues compiling x64 MacOS on an arm64 Mac, so for now I can only compile and deliver arm64 (M1/2/3) distributions. If anyone needs x64 (Intel Macbook chips), reach out and we can discuss further. I will keep looking for a viable workaround.

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.11.2...v0.11.3

- JavaScript
Published by j-berg about 2 years ago

metaboverse - Metaboverse-v0.11.2

What's Changed

  • Entity mapping improvements so user can select between standard display names and user-provided names for metabolites (by @j-berg in https://github.com/Metaboverse/Metaboverse/pull/153)
  • Fixes to error on window close (by @j-berg in c3f153aec78d354ace178cf4b8bf6403a6bc9c60)

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.11.1...v0.11.2

- JavaScript
Published by j-berg over 2 years ago

metaboverse - Metaboverse-v0.11.1

  • Fixes issues with HMDB ID mapping in back-end (#144, #146)
  • Prints note about using HMDB IDs with MetaboAnalyst API (#144)
  • Updates MetaboAnalyst API address for metabolite name conversion (#144)
  • Reverts to using Reactome metabolite names for visualization (will give the option in the future - #151, but need to handle cases where HMDB IDs are used as these are not very useful for visualization)
  • Updated documentation specifying that Ensembl transcript IDs or names should be used as Ensembl gene IDs do not work well. (#146)

What's Changed

  • V0.11.1 by @j-berg in https://github.com/Metaboverse/Metaboverse/pull/152

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.11.0...v0.11.1

- JavaScript
Published by j-berg over 2 years ago

metaboverse - Metaboverse-v0.11.0

What's Changed

  • Include scripts to automatically build release across platforms by @j-berg in https://github.com/Metaboverse/Metaboverse/pull/136
  • FDR fix & electron compatibility bumps by @j-berg in https://github.com/Metaboverse/Metaboverse/pull/143
  • Add more data checking for errors (see issues #128, #129, #130, #131)

We are trying to get a better sense of how we can best continue to develop Metaboverse for the community. If you are using Metaboverse, we would appreciate it if you took a few moments to fill out this survey: https://forms.gle/YdM1caZ7NhLAjxCGA. Thank you!

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.10.1...v0.11.0

- JavaScript
Published by j-berg almost 3 years ago

metaboverse - Metaboverse-v0.10.1

  • Updated license to MIT
  • Fixed version check when launching GUI to make sure it sorts version numbers correctly
  • Updated documentation (expanded walkthrough, added dev notes)
  • Added more test datasets distributed with each release
  • Added sample distribution display for Data Formatting tool
  • Fixes issue where collapsed reactions in other timepoints were not being highlighted

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.10.0...v0.10.1

- JavaScript
Published by j-berg over 3 years ago

metaboverse - Metaboverse-v0.10.0

What's Changed

  • Introduces Co-factor Selection, a drop-down menu available in Pattern Analysis. Selected a specific factor will limit the Pattern Analysis results to only the reactions containing the selected entity.
  • Implements a Pattern Analysis Table Export utility, whereby the user can export the Reaction Patterns of a given type.
  • Fixes an issue where some non-collapsed reactions were not showing up in Pattern results.

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.9.0...v0.10.0

- JavaScript
Published by j-berg almost 4 years ago

metaboverse - Metaboverse-v0.9.0

| Note: Files curated and analyzed using Metaboverse v0.9.0 will not be backward compatible with files generated using earlier versions of Metaboverse. | | --- |

Major - Integration of confidence values during data formatting, curation, and analysis. - Fixed issues during curation arising from updates to the formatting of Reactome source files.

Minor - Streamlined option buttons available during Pattern Analysis. - Force directed networks now have sticky nodes once a user a dragged them to a new position. - Added statistical thresholding visualization to Pattern Analysis module. - Output session file with each successful build - will have experiment name appended to file. - Sort Average reaction pattern by best statistic on each side of reaction - Fix reaction filtering to more strictly and flexibly remove transport reactions from reaction pattern categories, and to only display transport reactions in the TransReg reaction pattern category. - Node labels will default to the user-provided names if not the same as the curated default name.

Full Changelog: https://github.com/Metaboverse/Metaboverse/compare/v0.8.0...v0.9.0 , https://github.com/Metaboverse/metaboverse-cli/compare/v0.7.1...v0.9.0

- JavaScript
Published by j-berg over 4 years ago

metaboverse - Metaboverse-v0.8.0

| UPDATE (07 Feb 22): Previous issues with Reactome network building have been fixed for the upcoming release of Metaboverse! The Reactome annotation has changed, thus older versions of Metaboverse will no longer be able to create a fresh organism reaction network. However, by default, Metaboverse will always rely on a pre-existing, stable curation unless otherwise specified - this is so that if a change in the Reactome codebase does occur, it should not affect current or previous versions of Metaboverse as long as an already-curated network file is used. | | --- |

Major

  • Added data formatting aid page (see issue #86).
  • Added ability to cross-reference metabolite names with MetaboAnalyst and find more compatible names (see issue #74).

Minor

  • Fixed issue where Metaboverse would not populate selected organism from drop-down if previously selected and the user returns to the page (see commit).
  • Fixed issue where Metaboverse would not show the Continue button on the Curation page if necessary inputs were previously selected and the user returns to the page (see commit).

Note:

This version of Metaboverse only makes changes to the user interface and its backend. Thus, Metaboverse v0.8.0 continues to use metaboverse-cli 0.7.1.

- JavaScript
Published by j-berg almost 5 years ago

metaboverse - Metaboverse-v0.7.1

Important Notes

  • After curating your data on the metabolic model, you may receive an alert saying it cannot load the file, but the progress bar will show 100%. If you close the alert box and you see the button for the different analytical modules appear, you can ignore this warning. I am still working on diagnosing why this occasionally occurs and will hopefully have a solution soon.
  • Many of the changes introduced in v0.7.0 to session and intermediate file metadata will likely be incompatible with previous versions of Metaboverse.

Minor

  • Fix Session Data page to format variables, file paths better (see commit)
  • More flexible blocklist to capture all components with the same name, even if they have different species IDs (see commit1 ; commit2)
  • Find largest change possible for modifier regulation patterns (see commit)
  • Sort by best p-value (previously had taken a more conservative approach by using the worst p-value on each side of the reaction) (see commit)
  • Add button and capabilities to switch between inferred complex values or to compare each complex component individually within the reaction pattern (see commit1 ; commit2)
    • Will still display the complex as inferred value, but evaluated as each individual component during reaction pattern search
  • Protein complex inference/aggregation
    • mean -> median for generating aggregate magnitude value for protein complex from component parts (see commit)
    • Aggregate statistic calculated using e * gmean(p-array) (see commit)
    • Max aggregate p-value set to 1 (see commit)
  • Allow exporting line plots for time-course and multi-condition datasets (see issue #89)
  • Use user-provided names in labeling (see issue #87)
  • Toggle analyte labels on by default (see commit)
  • Allow flexibility for input data where commas are used in place of decimals (see issue #92)
  • Remove duplicate rows from input data (interactive input will warn about these) (see commit)
  • Fix Sustained reaction pattern to not identify is input and output value being compared are identical (see commit)
  • Fix issue with parseComponents() function where usage of modifiers in pattern determination was pushing all modifiers (catalysts and inhibitors) to reactants list (see commit)
  • For upregulated sustained reactions, get max of inputs and outputs (previously was getting min) (see commit)
  • Fixed global motif searching for pathway and perturbation visualization to search non-collapsed reaction dictionary too. (see commit)
  • Added reaction pattern tooltips on button to show a graphical example of each (see commit)
  • Move some shared utilities to the motif-utils.js file (see commit)

- JavaScript
Published by j-berg about 5 years ago

metaboverse - Metaboverse-v0.7.0

Important Note

Many of the changes introduced in v0.7.0 to session and intermediate file metadata will likely be incompatible with previous versions of Metaboverse.

Major

  • Enzyme/Metabolite reaction patterns added: The Enzyme reaction pattern evaluates for two neighboring reactions both with perturbed enzymes matching the given threshold. This will allow for better pattern identification, especially in RNA-seq/proteomics-only datasets. The Metabolite reaction pattern looks for neighboring reactions both with perturbed metabolites matching the given threshold (see issue #81).

Minor

  • Removed pathway-specific pattern detection: In our testing, these seemed to be minimally helpful.
  • Option added for users to define percentage of matching nodes between two reaction to allow for a collapse (see issue #82).
  • SVG export option (Full support for Inkscape, partial support for Illustrator) (see issue #83).
  • Improved and more explicit session data for all intermediate files (see issue #78).
  • Migrated source files to rutter.chpc.utah.edu/Metaboverse/source. This change should allow for faster downloads of pre-curated intermediate source files (see issue #80).
  • Loading icon in reaction pattern page to let user know patterns are loading, especially in cases where many reaction patterns are discovered and the software may take some time to display them all.

SHA256

e400c541ae66ef19d2192685a6b98b463e5498e27441bbbec34891f76b0b6141 ./Metaboverse-darwin-x64-0.7.0.zip c43472eb25eb1639e8e6266529b713b777c8e7dfb51e1ca21de6f4e6da8e0cc2 ./Metaboverse-linux-x64-0.7.0.zip 5c29c7a65a08540f523f2fa6dae5234423a27fc2ad3c55995f91feb7cb15cd53 ./Metaboverse-win32-x64-0.7.0.zip

- JavaScript
Published by j-berg about 5 years ago

metaboverse - Metaboverse-v0.6.0

Major

  • New database integration: First supported release with the ability to overlay data on BiGG and BioModels network models and enable reaction pattern searching across a wider array of organisms. Note: Network models from these sources can be less uniform as Reactome sources, so users should exercise some caution when using these capabilities and perform some sanity checks (see issue #73).
  • kNN visualization improved to allow for more stable NN building without error (see commit 2395cd6).
  • Neighbors dictionary backend curation is simplified and sped up (see commit 355abd4).
  • Improved security policies. Specifically, external websites are opened in an isolated browser window and explicitly are context isolated and unable to access node integration. Enabled GitHub and Reactome URLs (connect-src) are more specific (see commit 96b1c9f).

Minor

  • Progress bar during network build now update with more incremental steps for longer processes (see issue #77).
  • New variables for more unified backend processing. Metaboverse v0.6.0 and later will not be compatible with files curated using Metaboverse v0.5.0b or earlier.

- JavaScript
Published by j-berg about 5 years ago

metaboverse - Metaboverse-v0.5.0b

Metaboverse-v0.5.0b

  • macOS (64-bit): Metaboverse-darwin-x64-0.5.0b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.5.0b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.5.0b.zip

Important note

Starting in Metaboverse-v0.3.1b, organism curation files must end with the file extension .mvdb (previously .pickle) and final output files must end in .mvrs (previously .json). While changing the file extensions of old files may work, recent changes may no longer allow these older files to be compatible with newer versions of Metaboverse.

Major

  • Addresses issue #66, by hosting curated reference and template files for each organism per version of Metaboverse. Also provided user argument options to directly include already downloaded or curated files (--organism_curation_file, --neighbor_dictionary_file, --graph_template_file). Using pre-downloaded files, this reduced processing time for curating data on the human network from ~30-40 min to ~2 min. These pre-curated files will be processed with each release of Metaboverse and are hosted on SourceForge currently.

Minor

  • Fixes an issue where an empty unmapped dataframe would cause an error (fixed by #32e9283)
  • Fixes an issue the working path would be appended to the organism ID (fixed by #91a490d)
  • Addresses issue #67, where experiment name inputs with spaces would cause an error.
  • Bump required version of Electron to >=9.4.0 (see pull request #68).
  • Removed some unused user arguments from command-line interface.
  • Fixed an issue where the backend argument parse checker would try to append a file path to the organism ID.
  • Fixes internal warning for UI when CLI did not output blocklist or labels.
  • Updated copyright info.
  • Removed deprecated files.
  • Migrated from Travis-CI to GitHub Actions.

SHA256

87398db00903e3d86f02d7f6b1b581590d614240a51e95ae30ceea5aa8f332ba ./Metaboverse-darwin-x64-0.5.0b.zip 6865f00d0f4f1a1757f288dff8baa747ef726ebdb07d5e459424b54963843a90 ./Metaboverse-linux-x64-0.5.0b.zip d14c54e89fecf49586537eac93a4dbc22dae89f0e951661ea200eef43e9aacd1 ./Metaboverse-win32-x64-0.5.0b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.4.0b

Metaboverse-v0.4.0b

  • macOS (64-bit): Metaboverse-darwin-x64-0.4.0b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.4.0b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.4.0b.zip

Important note

Starting in Metaboverse-v0.3.1b, organism curation files must end with the file extension .mvdb (previously .pickle) and final output files must end in .mvrs (previously .json). While changing the file extensions of old files may work, recent changes may no longer allow these older files to be compatible with newer versions of Metaboverse.

Major

  • Partial reaction collapse: Addresses #51, which introduces partial collapsing to the reaction collapsing utility within Metaboverse. Previously, perfect matches were required between two reactions to collapse the reactions. However, this can be overly stringent in key metabolic pathways where a metabolite that is output by one reaction may not be required for the subsequent reaction (perhaps ATP is produced by reaction A but is not required for reaction B). To perform a partial collapse, Metaboverse operates by largely the same scheme as before, but now checks for a perfect match from each neighboring reaction, and if a perfect match is not available, checks for partial matches by filtering out high-degree nodes (quartile 98 of all non-reaction node degrees) and then checking if at least 30% of the nodes match with its neighbor.
  • Improvements to nearest neighbor searches where all iterations of a species are included in the graphing. Previously, it would only use the literally selected node to search for neighbors, but Reactome provides separate species IDs for a metabolite's different organelle-localizations, which was complicating these searches.

Minor

  • Displays a preview of the user-selected reaction in an interactive format on the Pattern Search Analysis page until the user selects a Pathway to visualize. If a reaction is collapsed and spans two pathways, no pathways will be shown and instead a note that the reaction spans two pathways is displayed.
  • The Pattern Search Analysis page now allows users to filter out collapsed reactions from the search results. By default, collapsed reactions will be displayed until the checkbox is unchecked by the user.
  • Minor updates to Pattern Search Analysis page to make better usage of blank space
  • Fixes #60, where the .mvrs file extension would not be automatically added to the user-provided output file name in Linux.
  • Addresses #62, where the some time-course/multi-condition slider bars would be improperly formatted.

SHA256

e91adf42a13f55bf4a17bbd2dcfab4dc911ee6ec6708ac79b807c8e55109d4f7 ./Metaboverse-darwin-x64-0.4.0b.zip f2593daf6cdaa32e5ca1f157fd0061cb381cac257d293fca36e73418c76b4be8 ./Metaboverse-linux-x64-0.4.0b.zip 0322a73a0d51a519f4b850808dd045f24a2c400539f80399678c9e6881d264b1 ./Metaboverse-win32-x64-0.4.0b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.3.3b

Metaboverse-v0.3.3b

  • macOS (64-bit): Metaboverse-darwin-x64-0.3.3b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.3.3b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.3.3b.zip

Important note

Starting in Metaboverse-v0.3.1b, organism curation files must end with the file extension .mvdb (previously .pickle) and final output files must end in .mvrs (previously .json). While changing the file extensions of old files may work, recent changes may no longer allow these older files to be compatible with newer versions of Metaboverse.

Minor updates

  • Closes #63 by applying safestr() function to all user input encodings to make sure no errors arise.

SHA256

019a65e76d9d342ee4e622b71c83af0ce25070040edcf29fcb74a89028e6f93b ./Metaboverse-darwin-x64-0.3.3b.zip 1df7e7648d1c4d1ab176d74366ccc9d81dd5637b671377cc09930f364a9805a8 ./Metaboverse-linux-x64-0.3.3b.zip b2472b1f5f8b7b0309334e7544fc80dbae3937e24b3f3a06bed7e749f91d8c63 ./Metaboverse-win32-x64-0.3.3b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.3.2b

Metaboverse-v0.3.2b

  • macOS (64-bit): Metaboverse-darwin-x64-0.3.2b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.3.2b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.3.2b.zip

Important note

Starting in Metaboverse-v0.3.1b, organism curation files must end with the file extension .mvdb (previously .pickle) and final output files must end in .mvrs (previously .json). While changing the file extensions of old files may work, recent changes may no longer allow these older files to be compatible with newer versions of Metaboverse.

Minor updates

  • Closes #59 where non-ascii characters in reaction names would break the info extraction. Added a safe-string conversion utility to prevent ascii-character issues. 190939c02525c13e439352f57a732a6ea76ea305d19b6b10d67b7f6c7a9412dc ./Metaboverse-darwin-x64-0.3.2b.zip 7ce07eb6fc553383faa7625bb8f2aacf79781146afae187a4e847191816ec322 ./Metaboverse-linux-x64-0.3.2b.zip 08e1d376a4a9c2b69290198fdcd8682215bc1cb71fee817f92d8f4dba61615e0 ./Metaboverse-win32-x64-0.3.2b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.3.1b

Metaboverse-v0.3.1b

  • macOS (64-bit): Metaboverse-darwin-x64-0.3.1b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.3.1b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.3.1b.zip

Important note

Starting in Metaboverse-v0.3.1b, organism curation files must end with the file extension .mvdb (previously .pickle) and final output files must end in .mvrs (previously .json). While changing the file extensions of old files may work, recent changes may no longer allow these older files to be compatible with newer versions of Metaboverse.

Minor updates

  • Fixes path separator for motif page name identification to allow for including modifiers in motif ID and exclusion of hubs (#55)
  • Fixes CHEBI mapping so that CHEBI IDs provided as input data are more reliably used as mapping IDs if it cannot match the metabolite by name (#58)
  • Fixes issue that arose in v0.3.0b where some motif stamps could not be clicked on for viewing for timecourse/multi-condition data where it could not identify the shape for an unknown component type (#54)
  • Tries to address (#59) where non-ascii characters in reaction names would break the info extraction. Was not able to recapitulate the error, but this fix, where relevant reaction metadata is forced to a string data-type, should allow for some flexibility here. This is still a problem on macOS only, will continue working on for v0.3.2b.
  • Updates walkthroughs and documentation to address (#31) and update formatting

4e76462948a1036dc08743cb91f0188ca967cfdb09a3768764290cbd99b51373 ./Metaboverse-darwin-x64-0.3.1b.zip 5795344208391ccd19179345acb18f9a5f05a823a4e329e0eb8eeffa604265a3 ./Metaboverse-linux-x64-0.3.1b.zip cb79eb39b81ec890b17b495b9073577191b79626f86d49441f9f5a9746a4cbcf ./Metaboverse-win32-x64-0.3.1b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.3.0b

Metaboverse-v0.3.0b

  • macOS (64-bit): Metaboverse-darwin-x64-0.3.0b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.3.0b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.3.0b.zip

Major updates

  • Allows for more flexible gene/protein mapping with Reactome-formatted node names. For example, Reactome will label a gene or protein with its isomer coordinates. Metaboverse now ignores those coordinates during attribute mapping of the user’s data.
  • New naming of modules: Motif Search is now called Pattern Analyis, Visualize is now called Explore, and Connectivity is now called Perturbation Networks. Changed to be more descriptive and accessible to all users from broader backgrounds

Minor updates

  • Fixed nearest neighbors capabilities in Perturbation Network visualization. In a previous release, a change had interfered with its function.
  • Use of outdated version will now direct user to the download page for the most recent version
  • The Back button from any of the analysis modules will now redirect back to the index page
  • Removed compartment visualization from the Perturbation Networks page as these often would just clutter the visualization and would not actually be helpful
  • Fixed reaction node formatting to turn off motif symbols/highlighting when timepoint/condition changed as this had been disabled by a previous change
  • Fixed collapsed reactions to ensure they were included in all reaction and motif formatting events
  • General formatting changes
  • Updated documentation

SHA256
585f03c3c521a0f8efc577f9f3df06fb90f11a3032b1b8a1ebd3c1be380e5f59 ./Metaboverse-darwin-x64-0.3.0b.zip 0a1ea991e49cb6848dae451e99d6f8ce013bc6a6e7a5df952b6a483417b4eb1d ./Metaboverse-win32-x64-0.3.0b.zip

- JavaScript
Published by j-berg over 5 years ago

metaboverse - Metaboverse-v0.2.0b

Metaboverse-v0.2.0b

  • macOS (64-bit): Metaboverse-darwin-x64-0.2.0b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.2.0b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.2.0b.zip

Major updates

  • Fixes issues with missing metabolites during the network mapping stage ( #37 ). Addressed by re-working the metabolite synonym scheme to provide the same coverage of synonym look-up as before, but with more robustness so that some that were difficult to map would start mapping (i.e., Fructose).
  • Added dynamic line-plots of a selected reaction motif for time-course and multi-condition data ( #15 ). When exploring motifs on the Motif page for time-course and multi-condition experiments, a new panel appears at the bottom of the page which, for a selected motif, will show those reaction motif's component's behavior across all the time-points or conditions.
  • Added the option to exclude reaction motifs at a given time-point or condition that appear in another selected time-point or condition. ( #16 ). For example, if a user has selected to view motifs at a terminal time-point, but they want to know which reactions are motifs at this time-point but not at the initial time-point, they can exclude the motifs that show up at both time-points using the appropriate drop-down menu on the motif page.

Minor updates

  • Metaboverse now outputs a table of unmapped metabolites ( #35 )
  • Added flexible search for metabolites in user data starting with "N-" or "n-"
  • Allow flexible directory deletion for Windows (prevent permissions issues)
  • Added duplicate row removal from user data and provide a warning to the user in the session info file
  • Unify compartment name variable in network database
  • Updated tests for metabolite mapping changes and includes a full network build test

SHA256
35c271031731169a26305991a3470163d715ea6bfdc9c8fdcbae3b53f12a5439 ./Metaboverse-darwin-x64-0.2.0b.zip e41b519503dd765f1ad4174ea2174df372857794c28e35151969228421a252f8 ./Metaboverse-linux-x64-0.2.0b.zip f9e577a3f3f54496a263ea9679a55dbc1749e02c01687ed47865ee3cea6f9775 ./Metaboverse-win32-x64-0.2.0b.zip

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - Metaboverse-v0.1.4b

Metaboverse-v0.1.4b

  • macOS (64-bit): Metaboverse-darwin-x64-0.1.4b.zip
  • Windows (64-bit): Metaboverse-win32-x64-0.1.4b.zip
  • Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.1.4b.zip

Updates:

  • Fixes #42, where an error log is output if build fails
  • Removes direct Matplotlib imports in metaboverse-cli modules to prevent unnecessary errors and incompatibilities

Checksums (SHA256):

  • Metaboverse-darwin-x64-0.1.4b.zip: 80928204e6e31359c61240c8197948bf9f9f6c2b0eeeccebda8af76d8a02d5fb
  • Metaboverse-linux-x64-0.1.4b.zip: 2eade60c071d0913429e2b3cab6bcd0732a77dc9f5205a9242d6bacaec6951bc
  • Metaboverse-win32-x64-0.1.4b.zip: 692a09b0ddc90044c935670c348e0ef1dcf531ed8254075e6526b7ef3a426eb2

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - Metaboverse-v0.1.3b

Metaboverse-v0.1.3b

Initial user-ready beta release to accompany pre-print - macOS (64-bit): Metaboverse-darwin-x64-0.1.3b.zip - Windows (64-bit): Metaboverse-win32-x64-0.1.3b.zip - Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.1.3b.zip

Updates:

  • Fixes #25, where spaces were unable to be used in user input file paths
  • Fixes #27, where admin mode was required for some file downloads
  • Also implements more flexible path accession between macOS and Windows path formatting

Current Features Available:

  • Motif search
  • General visualization
  • Perturbation connectivity analysis
  • kNN networks

Checksums (SHA256):

  • Metaboverse-darwin-x64-0.1.3b.zip: cf443176e4f3ca1b2a7021e9647cc7604eb107907efa6d0b76ea470cdfb4130e
  • Metaboverse-linux-x64-0.1.3b.zip: 21c9c304a1020dc7463eda50b7bf0f3bef7aaa7c05de5a376d0b44ded39068ba
  • Metaboverse-win32-x64-0.1.3b.zip: 407cb06165e08d3b1dba227f681f149cbfb2827124cf308396624c8d0d324bda

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - Metaboverse-v0.1.2b

Metaboverse-v0.1.2b

Initial user-ready beta release to accompany pre-print - macOS (64-bit): Metaboverse-darwin-x64-0.1.2b.zip - Windows (64-bit): Metaboverse-win32-x64-0.1.2b.zip - Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.1.2b.zip

Updates:

  • Fixes bug that prevented the curation from running without a blocklist ( #19 )
  • Fixes bug during data mapping that caused protein or gene values to occasionally map to metabolites ( #20 )

Current Features Available:

  • Motif search
  • General visualization
  • Perturbation connectivity analysis
  • kNN networks

Checksums (SHA256):

  • Metaboverse-darwin-x64-0.1.2b.zip: d3014475eb3c385fd489d4ec23b620939c30dbee263ad95b7f5f8037ca7bb8f6
  • Metaboverse-linux-x64-0.1.2b.zip: e60af6db0b45e36f158af73852538601b4fb2c72edd9af0bb973b7f3090c2a30
  • Metaboverse-win32-x64-0.1.2b.zip: 4a9766eecf863c8d10a13c07df7d527f23a5dc9e7ddfa2ef1b5574f9c1ae4b16

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - Metaboverse-v0.1.1b

Metaboverse-v0.1.1b

Initial user-ready beta release to accompany pre-print - macOS (64-bit): Metaboverse-darwin-x64-0.1.1b.zip - Windows (64-bit): Metaboverse-win32-x64-0.1.1b.zip - Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.1.1b.zip

Updates:

  • Fixes minor run-time issues with the Metaboverse interactive app
  • Fixes version alert to let users know if there is a newer version of Metaboverse available

Current Features Available:

  • Motif search
  • General visualization
  • Perturbation connectivity analysis
  • kNN networks

Checksums (SHA256):

  • Metaboverse-darwin-x64-0.1.1b.zip: dab11cfc179644cb46a885e11e7c6c71f001336509876e23c5dcaef8d57713a8
  • Metaboverse-linux-x64-0.1.1b.zip: 08734c56eeb45ff1218869d3e9b6cdbc2d888c89a013b63c2bbb6231c8834e61
  • Metaboverse-win32-x64-0.1.1b.zip: 4817c3997a64a3460fe95ac429de2ed1b03c031f439e4a20fcb32226e1a3adca

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - Metaboverse-v0.1.0b

Metaboverse-v0.1.0b

Initial user-ready beta release to accompany pre-print - macOS (64-bit): Metaboverse-darwin-x64-0.1.0b.zip - Windows (64-bit): Metaboverse-win32-x64-0.1.0b.zip - Linux/Ubuntu (64-bit): Metaboverse-linux-x64-0.1.0b.zip

Current Features Available:

  • Motif search
  • General visualization
  • Perturbation connectivity analysis
  • kNN networks

Checksums (SHA256):

  • Metaboverse-darwin-x64-0.1.0b.zip: 2eec06fa62c17095310f80c4faa7adeb5b6d997e9fc221acbce209534c214859
  • Metaboverse-linux-x64-0.1.0b.zip: 8ef2a2b80e82b5318461c8aafd3f89f1ec578940945dbf394ae07e2fbd02b9c9
  • Metaboverse-win32-x64-0.1.0b.zip: e91dc324e74ba7a949c584b0d16ea814b496969bae28e8a27ae6ed7ba512c19d

- JavaScript
Published by j-berg almost 6 years ago

metaboverse - metaboverse-v0.0.1b

Demo pre-release with included human network data file for network visualization and exploration. Currently only available for MacOS.

How to run: 1. Download attached .zip demo file. 2. Double-click on .zip file to uncompress Metaboverse and the accompanying test file 3. Within the uncompressed folder, right-click on Metaboverse to launch the app 4. Drag and drop the .json file to the appropriate load icon and click the Visualize button.

- JavaScript
Published by j-berg over 6 years ago