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Recent Releases of https://github.com/akikuno/tsumugi-dev

https://github.com/akikuno/tsumugi-dev - 0.3.2

v0.3.2 (2025-06-23)

💥 Breaking Changes

  • Updated to support IMPC Release 23.0
    Upgraded the underlying dataset to the latest IMPC Release 23.0 for improved data coverage and accuracy.
    Issue: #88
    [Commit Detail]

🌟 New Features

  • Human disease gene highlighting
    Added functionality to highlight genes associated with human diseases, enabling researchers to identify disease-relevant gene modules within phenotypic networks. The feature uses Phenodigm algorithm to establish mouse-human disease relationships.
    Issue: #87
    [Commit Detail]
    Thanks to @kinari-labwork for contributing to this issue!

🖼️ User Interface

  • Enhanced footer layout
    Redesigned the footer to better emphasize documentation and inquiry options, improving user access to help resources.
    Issue: #98
    [Commit Detail]

  • Unified mobile control panel
    Consolidated the previously split left/right control panels into a single, unified panel view on mobile devices for improved usability and screen space utilization.
    Issue: #89
    [Commit Detail]

  • Dynamic header font sizing
    Implemented responsive header font sizing that automatically adjusts on mobile devices to ensure text displays properly within a single line, preventing layout issues.
    Issue: #93
    [Commit Detail]

🐛 Bug Fixes

  • Fixed mobile toggle button visibility
    Resolved an issue where the toggle close button was not appearing on mobile devices, restoring proper navigation functionality.
    Issue: #94
    [Commit Detail]

  • Optimized network rendering performance
    Implemented a performance optimization by limiting the maximum number of displayed nodes to 150 (reduced from 200) to prevent rendering delays and ensure smooth user experience with large networks.
    Issue: #103
    [Commit Detail]

  • Improved gene symbol page visualization
    Modified gene symbol pages to display only nodes that are directly connected to the target gene, reducing visual clutter and focusing on relevant gene relationships.
    Issue: #104
    [Commit Detail]

🔧 Maintenance

  • Enhanced raw data distribution
    Added version tags to TSUMUGI_raw_data filenames and expanded format support to include both CSV and Parquet formats, improving data accessibility and compatibility with different analysis tools.
    Issues: #95, #96
    [Commit Detail]

  • Streamlined deployment workflow
    Consolidated the separate testing and production deployment notebooks into a single, unified deployment file, simplifying the release process and reducing maintenance overhead.
    Issue: #101
    [Commit Detail]

- JavaScript
Published by akikuno 8 months ago

https://github.com/akikuno/tsumugi-dev - 0.3.1

🖼️ User Interface

  • The user-specified phenotype is now always displayed, regardless of filter settings
    Issue #80
    [Commit Detail]

  • Added TSUMUGI version information and a contact form to the footer
    Issue #79
    [Commit Detail]

🐛 Bug Fixes

  • Ensured that all nodes and edges related to the target phenotype are properly displayed
    Issue #54
    [Commit Detail]

  • To prevent nodes from disappearing when adjusting the slider, the row with the largest absolute effect size (between Homo and Hetero) is now selected
    Issue #72
    [Commit Detail]

  • edgeMin is now defined as the minimum edge size among edges connected to the target gene, similar to the edgeMax logic
    Issue #74
    [Commit Detail]

  • Nodes that do not contain the user-specified phenotype are now excluded from display
    Issue #54
    [Commit Detail]

  • Only edges between nodes that share two or more phenotypes are now visualized
    Issue #81
    [Commit Detail]

  • Fixed an issue where duplicate phenotypes were shown in tooltips
    Issue #82
    [Commit Detail]

🔧 Maintenance

  • Improved visibility in gene search by automatically centering and zooming in on the corresponding node
    Issue #78
    [Commit Detail]
    Thanks for your comments, @aki2274!

- JavaScript
Published by akikuno 10 months ago

https://github.com/akikuno/tsumugi-dev - 0.3.0

💥 Breaking

  • Annotate the four life stages: Embryo, Early, Interval, and Late. Issue #20.

  • Set thresholds for visualization considering similarity. Issue #77. [Commit Detail].

    • Thanks to @aki2274 for reporting this issue!

  • Rename the header name cluster to module in the exported CSV. [Commit Detail].

📝 Documentation

  • Add documentation on how to load the last column (List of shared phenotypes) in TSUMUGI_raw_data.csv.gz as list[str]. [Commit Detail].

  • Add documentation of life stage. [Commit Detail].

🖼️ User Interface

- JavaScript
Published by akikuno 10 months ago

https://github.com/akikuno/tsumugi-dev - 0.2.2

🖼️ User Interface

📝 Documentation

  • Publish a complete list of currently available phenotypes and genes.
    Issue: #34
    Commit Detail

🔧 Maintenance

  • Use inherit for tab button text color to ensure consistent appearance and prevent default blue styling on macOS.
    Issue: #67
    Commit Detail

  • Unify HTML templates for better maintainability.
    Issue: #68
    Commit Detail

  • Unify JavaScript templates to reduce redundancy.
    Issue: #69
    Commit Detail

🐛 Bug Fixes

  • Adjust the severity slider behavior to always keep at least one gene pair visible, even at minimum or maximum values.
    Issue: #72
    Commit Detail

  • Change the link button font color from blue to black (#333) on macOS for consistent styling.
    Issue: #67
    Commit Detail

- JavaScript
Published by akikuno 11 months ago

https://github.com/akikuno/tsumugi-dev - 0.2.1

📝 Documentation

🌟 New Features

  • Add a Google Form to allow anyone to submit inquiries. [Commit Detail]

  • Add a search box for a gene symbol in the network Issue. #30 [Commit Detail]

    🐛 Bug Fixes

  • Modified to ensure that the Submit button is definitely disabled when the input is empty. Issue: #61 [Commit Detail]

  • Phenotypes for which no phenotype-similar gene groups were detected have been removed from available_mp_terms.json to prevent them from being selected. Issue: #58 [Commit Detail]

  • Fixed a bug where target genes disappeared when increasing the slider threshold in "Gene". Issue: #63 [Commit Detail]

🖼️ User Interface

- JavaScript
Published by akikuno 11 months ago

https://github.com/akikuno/tsumugi-dev - 0.2.0

💥 Breaking

  • Allow users to input their intended gene lists. Issue #42 [Commit Detail]

🐛 Bug Fixes

🔧 Maintenance

- JavaScript
Published by akikuno 11 months ago

https://github.com/akikuno/tsumugi-dev - 0.1.5

🔧 Maintenance

  • The previously separated phenotypeForm and geneForm have been unified. [Commit Detail]

  • For code reusability, the function has been moved to an external module.

🖼️ User Interface

  • searchForm has been repositioned at the top and made scrollable when necessary to prevent it from being cut off on smaller screens. [Commit Detail]

  • Make the favicon display correctly in Firefox. [Commit Detail]

- JavaScript
Published by akikuno 11 months ago

https://github.com/akikuno/tsumugi-dev - 0.1.4

v0.1.4 (2025-03-03)

🐛 Bug Fixes

🔧 Maintenance

  • Ensure that the line endings of the raw data are LF. Issue: #50 [Commit Detail]

  • For code reusability, the function has been moved to an external module.

- JavaScript
Published by akikuno 12 months ago

https://github.com/akikuno/tsumugi-dev - 0.1.3

v0.1.3 (2025-02-27)

💥 Breaking

🌟 New Features

  • Add checkbox of genotype and sex specificity. Issue: #22 [Commit Detail]

  • Add Download raw data button for re-use of the TSUMUGI data. Issue: #47 [Commit Detail]

🖼️ User Interface

  • Modify the slider text and numbers to be displayed in a single column. [Commit Detail]

  • Hide the Phenotype severity slider if the phenotype is binary (all effect sizes are 1). Issue #46 [Commit Detail]

🔧 Maintenanc

  • Add a function to manage the completion of data retrieval. [Commit Detail]

  • Download Raw data from CloudFlare R2 repository. Issue: #47 [Commit Detail]

  • Use a directory structure that separates Data and Frontend. Issue: #48 [Commit Detail]

- JavaScript
Published by akikuno 12 months ago

https://github.com/akikuno/tsumugi-dev - 0.1.2

🌟 New Features

  • Specify Homo, Hetero, or Hemi for each phenotype. Issue: #38 [Commit Detail]

  • Indicate whether each phenotype is male- or female-specific. Issue: #22 [Commit Detail]

🖼️ User Interface

🐛 Bug Fixes

  • The number of nodes was set to 200 (arbitrary) because too many nodes would make rendering impossible. Issue: #45 [Commit Detail]. Many thanks to Dr. Hayate Suzuki (University of Tsukuba) for reporting this issue!

## 🔧 Maintenance

  • Compress JSON files with Gzip to reduce server usage. Issue: #24 [Commit Detail]

- JavaScript
Published by akikuno about 1 year ago

https://github.com/akikuno/tsumugi-dev - 0.1.1

💥 Breaking

🖼️ User Interface

  • Change the placeholder of TSUMUGI. Issue: #32 [Commit Detail]

  • Change "Similarity of accessory phenotypes" and "Severity of target phenotype" to "Phenotypes similarity" and "Phenotype severity". Issue: #35 [Commit Detail]

🔧 Maintenance

  • Decompose Cytoscape's Tooltip handler into functions for each element. [Commit Detail]

  • Change the directory name from web to TSUMUGI Issue: #31 [Commit Detail]

- JavaScript
Published by akikuno about 1 year ago

https://github.com/akikuno/tsumugi-dev - 0.1.0

Genes of interest can now be selected.

- JavaScript
Published by akikuno over 1 year ago

https://github.com/akikuno/tsumugi-dev - 0.0.1

Open the production environment 🚀 https://www.md.tsukuba.ac.jp/LabAnimalResCNT/TSUMUGI/

- JavaScript
Published by akikuno over 1 year ago