DNAnalyzer v3.5.0-beta.0

[VerisimilitudeX]

Introduction

This release introduces full batch FASTA file support, quantitative insights into disease-associated gene expression sites, annotations for CFTR sequences, and parallelized codon mapping for even faster data processing. Additionally, it addresses several major compatibility bugs on Linux and uses Multi-Task Learning (MTL) to further improve performance by learning multiple machine learning tasks at the same time.

DNAnalyzer currently takes just 11 minutes to conduct analyses on a full human genome running on an M4 Max MacBook Pro, a 47% reduction on average from v3.0.0-beta.0. The end goal for DNAnalyzer is to be able to run on a mobile device in mere seconds.

Of course, this release would not have been possible without contributions from the computational biology research community, and we are grateful to the 43 returning and first-time contributors for their commits, discussion posts, and issues. Please continue reading for more updates and the full change log.

Updates to Citations

If you utilize this software for personal, institutional, or company purposes, please cite DNAnalyzer using:

Acharya, P. (2022). Democratizing ML-powered DNA analysis through efficient on-device analysis and interpretive tools. (Version 3.5.0-beta.0) [Computer software]. https://github.com/VerisimilitudeX/DNAnalyzer

What's Changed

Features

• Genes and analysis parameters by @i2kmt in #379
• Make a full FASTA implementation by @Nv7-GitHub in #391
• Add basic FastQ implementation by @Nv7-GitHub in #399
• Genes and their evolutionary background involved in diseases by @VerisimilitudeX in #398
• CFTR Sequence by @Karzinisierung in #406
• CFTR Annotations by @Karzinisierung in #408

Fixes

• Fixes Undocumented class found JAVA-D1000 by @VerisimilitudeX in #392
• Fix broken lines of code badge by @VerisimilitudeX in #393
• Fix RBC error from Grace C by @VerisimilitudeX in #418
• Fix Deepsource issues for (JAVA-S1050) Non-final static fields should not be public #422 by @ishche in #424

Code Improvements

• Parallelize build codon map by @garyglatfelter in #407
• Switch to personal PayPal by @VerisimilitudeX in #389
• Update goals by @VerisimilitudeX in #388

Documentation Updates

• Add Armaan to citation by @VerisimilitudeX in #412
• Update README.md by @IcebergSnow in #414
• Fix typos and broken links in contribution guides by @taylorreiter in #425

Styling and Formatting

• Style: format code with Autopep8 and Google Java Format by @deepsource-autofix in #450 and other PRs.
• [ImgBot] Optimize images by @imgbot in #396

Miscellaneous

• Better Linux instructions for downloading by @LimesKey in #390
• Create codeql.yml by @VerisimilitudeX in #404
• Intro Spring Boot by @MartinGallauner in #427

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New Contributors

• @i2kmt made their first contribution in #379
• @Karzinisierung made their first contribution in #406
• @IcebergSnow made their first contribution in #413
• @taylorreiter made their first contribution in #425
• @Mrigankkh made their first contribution in #431

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Full Changelog: v3.0.0-beta.0...v3.5.0-beta.0

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This discussion was created from the release DNAnalyzer v3.5.0-beta.0.

[IcebergSnow]

Awesome! This is perfect for getting metrics quickly for my gene expression project!

[VerisimilitudeX]

Glad to hear, @IcebergSnow.