Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of dnanalyzer

dnanalyzer - Add mutation functionality w/ FASTA formatting

What's Changed

  • Add visuals to the website by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/471
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/468
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/465
  • Create a DNAMutation class to mutate DNA sequences by @Paucey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/460
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/473

New Contributors

  • @Paucey made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/460

Full Changelog: https://github.com/VerisimilitudeX/DNAnalyzer/compare/v3.6.0...v3.6.1

- HTML
Published by VerisimilitudeX about 1 year ago

dnanalyzer - Overhauled Website + Web-Based DNA Analysis

Arc 2025-02-10 01 51 05

Try it now. The website is currently in the alpha stage of development, and so there are numerous bugs present.

What's Changed

  • Adds a background video to the website by @ArchontisKostis in https://github.com/VerisimilitudeX/DNAnalyzer/pull/336
  • JAVA-D1001 adds javadoc to method by @MartinGallauner in https://github.com/VerisimilitudeX/DNAnalyzer/pull/322
  • Unnecessary imports removed. by @Rishav1707 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/346
  • Revert "Unnecessary imports removed." by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/349
  • Boolean literal is redundant. by @Rishav1707 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/347
  • Fix unsafe usage of getResource by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/335
  • Add Additional testcases by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/340
  • Adds test case for launching the GUI by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/350
  • Update Gradle from V2 --> V2.3.3 by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/351
  • Automatic downloading, Automatic GUI display, Automatic Gradlew building in one simple executable file by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/339
  • Deepsource Wrong argument order in test assertions fix by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/353
  • Add Rating GUI by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/355
  • Executable installer and GUI launcher by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/354
  • Changed wording prompt to allow for better understanding for ChatGpt by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/365
  • Updating Java download link by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/366
  • [AI] Human-friendly Analysis by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/364
  • Update README.md by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/363
  • New Feature - AI Analysis by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/369
  • refactor: Use stream.allMatch in isRandomDNA by @xlxs4 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/374
  • Remove Wakatime by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/376
  • Update goals by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/388
  • Genes and analysis parameters by @i2kmt in https://github.com/VerisimilitudeX/DNAnalyzer/pull/379
  • Switch to personal PayPal by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/389
  • Better Linux instructions for downloading by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/390
  • Make a full FASTA implementation by @Nv7-GitHub in https://github.com/VerisimilitudeX/DNAnalyzer/pull/391
  • Fixes Undocumented class found JAVA-D1000 by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/392
  • Remove broken lines of code badge by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/393
  • ci: Update .deepsource.toml by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/394
  • format code with google-java-format and autopep8 by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/395
  • [ImgBot] Optimize images by @imgbot in https://github.com/VerisimilitudeX/DNAnalyzer/pull/396
  • format code with google-java-format and autopep8 by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/397
  • Add basic FastQ implementation by @Nv7-GitHub in https://github.com/VerisimilitudeX/DNAnalyzer/pull/399
  • format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/401
  • format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/403
  • Genes and their evolutionary background that are involved in diseases by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/398
  • Create codeql.yml by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/404
  • Parallelize build codon map by @garyglatfelter in https://github.com/VerisimilitudeX/DNAnalyzer/pull/407
  • Update codeql.yml by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/410
  • format code with google-java-format and autopep8 by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/409
  • CFTR Sequence by @Karzinisierung in https://github.com/VerisimilitudeX/DNAnalyzer/pull/406
  • CFTR Annotations by @Karzinisierung in https://github.com/VerisimilitudeX/DNAnalyzer/pull/408
  • Add Armaan to citation by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/412
  • Update DNAAnalysis.java by @IcebergSnow in https://github.com/VerisimilitudeX/DNAnalyzer/pull/413
  • Update README.md by @IcebergSnow in https://github.com/VerisimilitudeX/DNAnalyzer/pull/414
  • Fix RBC error from Grace C by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/418
  • fix typos and broken links in contribution guides by @taylorreiter in https://github.com/VerisimilitudeX/DNAnalyzer/pull/425
  • Intro spring boot by @MartinGallauner in https://github.com/VerisimilitudeX/DNAnalyzer/pull/427
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/428
  • Fix Deepsource issues for #422 by @ishche in https://github.com/VerisimilitudeX/DNAnalyzer/pull/424
  • Added documentation to undocumented methods by @Mrigankkh in https://github.com/VerisimilitudeX/DNAnalyzer/pull/431
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/432
  • Added description for param tags. by @Mrigankkh in https://github.com/VerisimilitudeX/DNAnalyzer/pull/433
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/434
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/436
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/437
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/438
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/440
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/441
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/442
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/444
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/443
  • Update README.md by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/446
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/451
  • style: format code with Autopep8 and Google Java Format by @deepsource-autofix in https://github.com/VerisimilitudeX/DNAnalyzer/pull/450

New Contributors

  • @MartinGallauner made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/322
  • @Rishav1707 made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/346
  • @xlxs4 made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/374
  • @i2kmt made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/379
  • @Karzinisierung made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/406
  • @IcebergSnow made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/413
  • @taylorreiter made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/425
  • @Mrigankkh made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/431

Full Changelog: https://github.com/VerisimilitudeX/DNAnalyzer/compare/v2.1.1...v3.6.0

- HTML
Published by VerisimilitudeX about 1 year ago

dnanalyzer - DNAnalyzer v3.5.0-beta.0

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:

py 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 #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

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

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

- HTML
Published by VerisimilitudeX about 1 year ago

dnanalyzer - Meet DNAI: A ML-Based Analysis of DNA

Note: Some features mentioned below will be rolling out to users over the next couple of weeks as we haven't finished verifying its reliability

Today, we are proud to introduce DNA.I., a groundbreaking open source project that brings the power of machine learning to DNA analysis. DNAnalyzer is the first and only tool that lets you explore, understand, and discover the secrets of your DNA sequences with ease and elegance. DNAnalyzer is built on DNA.I., a revolutionary ML-based framework that can reveal the hidden patterns and properties of DNA sequences, such as gene expression, methylation, transcription factors, and more.

DNA.I. uses cutting-edge deep learning models and techniques to learn from massive genomic data and generate stunning insights. DNA.I. can also do amazing things like sequence alignment, motif discovery, and annotation. DNA.I. is designed to be flexible and modular, so you can tailor your analysis pipelines and integrate your own data sources.

Some of the amazing features of DNAnalyzer v3.0.0-beta.0 are: * A beautiful and intuitive graphical user interface (GUI) that lets you easily upload your DNA sequences, choose the analysis options, and see the results in gorgeous visualizations. * A powerful command-line interface (CLI) that gives you more control and functionality for those who love to work in a terminal environment. * A rich collection of pre-trained models and datasets that cover a wide range of DNA analysis tasks, such as gene expression prediction, methylation detection, transcription factor binding site identification, and more. * A comprehensive documentation that guides you through how to install, use, and extend DNAnalyzer and DNA.I. * A community forum where you can connect with other users, ask questions, share feedback, report issues, and contribute to the development of the project. * We believe that DNAnalyzer will be an invaluable and delightful resource for researchers, students, educators, and enthusiasts who want to explore the fascinating world of DNA. We welcome any suggestions, comments, or contributions that can help us make our project better and more accessible and beneficial for everyone.

To download the new DNAnalyzer, please visit our GitHub repository: https://github.com/VerisimilitudeX/DNAnalyzer/releases

To learn more about DNA.I. and how it works, please read our upcoming research paper (releasing on 8/31/2023): A ML-Based Analysis of DNA

As always, thank you for your support and interest in DNAnalyzer! 🧬

What's Changed

  • Adds a background video to the website by @ArchontisKostis in https://github.com/VerisimilitudeX/DNAnalyzer/pull/336
  • JAVA-D1001 adds javadoc to method by @MartinGallauner in https://github.com/VerisimilitudeX/DNAnalyzer/pull/322
  • Unnecessary imports removed. by @Rishav1707 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/346
  • Revert "Unnecessary imports removed." by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/349
  • Boolean literal is redundant. by @Rishav1707 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/347
  • Fix unsafe usage of getResource by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/335
  • Add Additional testcases by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/340
  • Adds test case for launching the GUI by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/350
  • Update Gradle from V2 --> V2.3.3 by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/351
  • Automatic downloading, Automatic GUI display, Automatic Gradlew building in one simple executable file by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/339
  • Deepsource Wrong argument order in test assertions fix by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/353
  • Add Rating GUI by @Ravina-Deogadkar in https://github.com/VerisimilitudeX/DNAnalyzer/pull/355
  • Executable installer and GUI launcher by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/354
  • Changed wording prompt to allow for better understanding for ChatGpt by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/365
  • Updating Java download link by @LimesKey in https://github.com/VerisimilitudeX/DNAnalyzer/pull/366
  • [AI] Human-friendly Analysis by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/364
  • Update README.md by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/363
  • New Feature - AI Analysis by @VerisimilitudeX in https://github.com/VerisimilitudeX/DNAnalyzer/pull/369
  • refactor: Use stream.allMatch in isRandomDNA by @xlxs4 in https://github.com/VerisimilitudeX/DNAnalyzer/pull/374

New Contributors

  • @MartinGallauner made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/322
  • @Rishav1707 made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/346
  • @xlxs4 made their first contribution in https://github.com/VerisimilitudeX/DNAnalyzer/pull/374

Full Changelog: https://github.com/VerisimilitudeX/DNAnalyzer/compare/v2.1.1...v3.0.0-beta.0

- HTML
Published by VerisimilitudeX almost 3 years ago

dnanalyzer - Website v2, Configure Sentry API, Other Minor Enhancements

What's Changed

  • Change tutorial video from OneDrive to Youtube by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/312
  • Update style.css by @a5a7 in https://github.com/Verisimilitude11/DNAnalyzer/pull/316
  • New web UI by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/317
  • Refactor Junit test classes and methods to be package-private by @Ravina-Deogadkar in https://github.com/Verisimilitude11/DNAnalyzer/pull/319
  • Add copyright headers and modify to 2023 by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/333

New Contributors

  • @a5a7 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/316

What's Next?

The project may seem to have been relatively quiet for the past couple of weeks, but in reality, the team has been hard at work revamping the project and recruiting new contributors. Stay tuned for more updates as we continue to incorporate machine learning into DNAnalyzer. Expect the next release to be a big one!

Downloading

To download the source files, expand the "Assets" section below and choose either the zip or tar.gz file, depending on your operating system. Once downloaded, you can run the program using the command line interface (CLI) commands explained in the README or via the new GUI.

Video tutorial on installation and usage: https://youtu.be/dOwkInn6eDw

As always, thanks everyone for your contributions! I'll see you all in the next release. 👋

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v2.1.0...v2.1.1

- HTML
Published by VerisimilitudeX about 3 years ago

dnanalyzer - Introducing An All-New GUI & Website

GUI

Thanks, @frankschmitt for implementing a cross-platform GUI application for DNAnalyzer. Currently, it supports the following features: - Set the name of the DNA file to analyze - Set minimum and maximum number of reading frames - Run analysis

The Met CLI continues to be the best way to run the program, with more features to be added to both in the future.

Website

Thanks, @krishnabiradar310802 for developing a website that creates awareness for DNAnalyzer and outlines the main features. It is accessible via https://www.dnanalyzer.live/ and is hosted on GitHub Pages. We are currently working on linking the backend to the frontend with the help of @aryanagrawal8808. @zackwebster and @BLUE-DEVIL1134 who are working on improving the frontend code.

As always, thanks, everyone for your contributions! I'll see you all in the next release.

What's Changed

  • Fixed bugs in README by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/201
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/200
  • Webpage by @krishnabiradar310802 in https://github.com/Verisimilitude11/DNAnalyzer/pull/202
  • Updated padding by @krishnabiradar310802 in https://github.com/Verisimilitude11/DNAnalyzer/pull/203
  • Refactor CodonDataConstants by @Kit-p in https://github.com/Verisimilitude11/DNAnalyzer/pull/194
  • Revert "Refactor CodonDataConstants" by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/209
  • Refactor CmdArgs.run() by @ishche in https://github.com/Verisimilitude11/DNAnalyzer/pull/196
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/211
  • Organize code into folders by @plopez26DPU in https://github.com/Verisimilitude11/DNAnalyzer/pull/214
  • Add Wiki markdown by @plopez26DPU in https://github.com/Verisimilitude11/DNAnalyzer/pull/217
  • Refactor CmdArgs by @singloon in https://github.com/Verisimilitude11/DNAnalyzer/pull/198
  • Refactor Properties.isRandomDNA(String) - Issue #73 by @B4CKF1SH in https://github.com/Verisimilitude11/DNAnalyzer/pull/97
  • Fix deploy GitHub page workflow by @Kit-p in https://github.com/Verisimilitude11/DNAnalyzer/pull/227
  • Changing wording, Gradle may not work with JDK 19. by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/235
  • Update CodonFrame.java by @sourabhkashyap95 in https://github.com/Verisimilitude11/DNAnalyzer/pull/213
  • refactor: protein finder by @boaglio in https://github.com/Verisimilitude11/DNAnalyzer/pull/216
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/221
  • Refactor CodonDataConstants by @LoicB in https://github.com/Verisimilitude11/DNAnalyzer/pull/233
  • Refactor output codons by @plopez26DPU in https://github.com/Verisimilitude11/DNAnalyzer/pull/234
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/238
  • About us page by @krishnabiradar310802 in https://github.com/Verisimilitude11/DNAnalyzer/pull/241
  • New CLI documentation by @plopez26DPU in https://github.com/Verisimilitude11/DNAnalyzer/pull/244
  • Added some new future improvements to the read.md by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/257
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/259
  • fixed typo in link by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/264
  • Added Dependabot Configuration by @jenistenxavier in https://github.com/Verisimilitude11/DNAnalyzer/pull/263
  • Refactored the methods relating to printing neucleotide count by @zaino97 in https://github.com/Verisimilitude11/DNAnalyzer/pull/253
  • Use const declarations for variables that are never reassigned by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/267
  • Count base pairs update by @garyglatfelter in https://github.com/Verisimilitude11/DNAnalyzer/pull/260
  • Refactorings of getAminoAcidMapping by @Speedro in https://github.com/Verisimilitude11/DNAnalyzer/pull/243
  • [ImgBot] Optimize images by @imgbot in https://github.com/Verisimilitude11/DNAnalyzer/pull/254
  • Fix For Broken CodeQL Java Analysis by @Speedro in https://github.com/Verisimilitude11/DNAnalyzer/pull/272
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/279
  • Adding information about DNA to README by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/282
  • Add .DS_Store to .gitignore by @ImpossibleReality in https://github.com/Verisimilitude11/DNAnalyzer/pull/288
  • 'toggle' is never reassigned. Use 'const' instead by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/281
  • Condensed code in countBasePairs as to resolve #274 by @garyglatfelter in https://github.com/Verisimilitude11/DNAnalyzer/pull/285
  • Issue 252 publish gradle package by @jaybob007 in https://github.com/Verisimilitude11/DNAnalyzer/pull/290
  • #270 Added highCoverageRegions call to CmdArgs by @jaybob007 in https://github.com/Verisimilitude11/DNAnalyzer/pull/284
  • Refactorings of DNAAnalysis.countBasePairs(String) by @Speedro in https://github.com/Verisimilitude11/DNAnalyzer/pull/278
  • Undocumented declaration found by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/292
  • Refactoring #276 by @salahhalkhoums in https://github.com/Verisimilitude11/DNAnalyzer/pull/287
  • Feature/add javafx gui #121 by @frankschmitt in https://github.com/Verisimilitude11/DNAnalyzer/pull/286
  • Code refactoring by @ArchontisKostis in https://github.com/Verisimilitude11/DNAnalyzer/pull/219
  • Refactor ProteinFinder.getProtein method by @Ravina-Deogadkar in https://github.com/Verisimilitude11/DNAnalyzer/pull/294
  • Updating correct wording for feature by @LimesKey in https://github.com/Verisimilitude11/DNAnalyzer/pull/304

New Contributors

  • @krishnabiradar310802 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/202
  • @ishche made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/196
  • @plopez26DPU made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/214
  • @singloon made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/198
  • @LimesKey made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/235
  • @sourabhkashyap95 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/213
  • @boaglio made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/216
  • @LoicB made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/233
  • @jenistenxavier made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/263
  • @zaino97 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/253
  • @garyglatfelter made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/260
  • @ImpossibleReality made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/288
  • @jaybob007 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/290
  • @salahhalkhoums made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/287
  • @ArchontisKostis made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/219
  • @Ravina-Deogadkar made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/294

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v2.0.0...v2.1.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing a CLI and Gradle Support

What's Changed

  • Use user input filename for analysis by @Kit-p in https://github.com/Verisimilitude11/DNAnalyzer/pull/85
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/86
  • Test DNA From GDV by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/87
  • Create codeql-analysis.yml by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/88
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/89
  • added Contributing_Guidelines.md file by @sumitbishti in https://github.com/Verisimilitude11/DNAnalyzer/pull/92
  • Update ProteinFinder.java by @aakash232 in https://github.com/Verisimilitude11/DNAnalyzer/pull/93
  • resolves #90: added and update java docs by @iamHrithikRaj in https://github.com/Verisimilitude11/DNAnalyzer/pull/100
  • Refactor for Utility classes - Issue #84 by @B4CKF1SH in https://github.com/Verisimilitude11/DNAnalyzer/pull/98
  • resolves #80: Refactor CoreExecutor.createProteinList(String,String) by @iamHrithikRaj in https://github.com/Verisimilitude11/DNAnalyzer/pull/101
  • Fixed formatting inconsistencies by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/102
  • Refactor CodonData class #69 by @shubhwip in https://github.com/Verisimilitude11/DNAnalyzer/pull/94
  • Revert "Refactor CodonData class #69" by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/110
  • Separate constants from static functions by @shubhwip in https://github.com/Verisimilitude11/DNAnalyzer/pull/109
  • Refactor ProteinFinder.getProtein with many args by @shubhwip in https://github.com/Verisimilitude11/DNAnalyzer/pull/99
  • Refactor ReadingFrames constructor by @shubhwip in https://github.com/Verisimilitude11/DNAnalyzer/pull/111
  • added min and max count User input at beginning of program. by @Lumary2 in https://github.com/Verisimilitude11/DNAnalyzer/pull/113
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/114
  • Get ReadingFrame from user input by @klurpicolo in https://github.com/Verisimilitude11/DNAnalyzer/pull/115
  • #74 refactoring of Properties.countNucleotides method by @Speedro in https://github.com/Verisimilitude11/DNAnalyzer/pull/116
  • Refactor getAminoAcid method with reduced branches by @androlover98 in https://github.com/Verisimilitude11/DNAnalyzer/pull/118
  • Fixed broken link for DNA Generator by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/120
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/119
  • Refactor getAminoAcid by @shubhwip in https://github.com/Verisimilitude11/DNAnalyzer/pull/112
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/124
  • resolves #68 : updated README.md by @iamHrithikRaj in https://github.com/Verisimilitude11/DNAnalyzer/pull/127
  • Closes #128 : handled infinite loop when file-path is incorrect by @iamHrithikRaj in https://github.com/Verisimilitude11/DNAnalyzer/pull/129
  • Switch to picocli by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/123
  • Move CoreExecutor code into CmdArgs by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/155
  • Protein finding by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/158
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/159
  • Reformatted by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/163
  • Updates readme to include cli by @aminisonya in https://github.com/Verisimilitude11/DNAnalyzer/pull/162
  • Fix #95: added code conventions by @sumitbishti in https://github.com/Verisimilitude11/DNAnalyzer/pull/161
  • Configure Gradle build. Implements #117. by @frankschmitt in https://github.com/Verisimilitude11/DNAnalyzer/pull/125
  • Make compile work + picocli as external dependency + fat jar by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/164
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/166
  • Document the CmdArgs class, resolves #169 by @bufutda in https://github.com/Verisimilitude11/DNAnalyzer/pull/172
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/174
  • Reverse option by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/167
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/177
  • Adding Gradle instructions in Read Me by @Saket2 in https://github.com/Verisimilitude11/DNAnalyzer/pull/175
  • removed instantiation of class with only static methods by @AbbasSalloum in https://github.com/Verisimilitude11/DNAnalyzer/pull/171
  • Updated contributors in main readme.md by @sb-decoder in https://github.com/Verisimilitude11/DNAnalyzer/pull/180
  • Added inline video, removed markdown by @zackrhodes86 in https://github.com/Verisimilitude11/DNAnalyzer/pull/192
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/179

New Contributors

  • @Kit-p made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/85
  • @sumitbishti made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/92
  • @aakash232 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/93
  • @iamHrithikRaj made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/100
  • @B4CKF1SH made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/98
  • @shubhwip made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/94
  • @Lumary2 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/113
  • @klurpicolo made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/115
  • @Speedro made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/116
  • @androlover98 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/118
  • @Nv7-GitHub made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/123
  • @aminisonya made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/162
  • @frankschmitt made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/125
  • @bufutda made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/172
  • @Saket2 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/175
  • @AbbasSalloum made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/171
  • @sb-decoder made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/180
  • @zackrhodes86 made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/192

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v1.2.2...v2.0.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - [MINOR] Introducing A Slightly Refined Algorithm

A major release is coming up soon, currently slated for a mid-October release. This is going to be the last stable release before the major update. Thorough testing was conducted on this refined algorithm to ensure its accuracy.

What's Changed

  • Add .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/39
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/40
  • Format code with prettier and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/41
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/52
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/54
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/53
  • [ImgBot] Optimize images by @imgbot in https://github.com/Verisimilitude11/DNAnalyzer/pull/58
  • Update .deepsource.toml by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/55
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/57
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/56
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/64
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/62
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/63
  • Format code with autopep8 and google-java-format by @deepsource-autofix in https://github.com/Verisimilitude11/DNAnalyzer/pull/66

New Contributors

  • @deepsource-autofix made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/39

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v1.2.1...v1.2.2

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing Performance Tests

What's Changed

  • Added time trackers by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/26
  • Updated logo by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/25

Known Issues

  • Gene(s) with the highest coverage doesn't work as expected in https://github.com/Verisimilitude11/DNAnalyzer/issues/11

How to download

  1. Download and extract DNAnalyzer.jar / DNAnalyzer.rar / DNAnalyzer.zip
  2. Open the extracted folder through an IDE
  3. Make sure that you have JDK 11 or above
  4. Run Main.java which can be found under the files folder

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v1.1.0...v1.1.5

Note: This release is for testing purposes only

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing Major Performance Boost

What's Changed

  • Speed up nucleotide count by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/26/commits/97a1b4d2d217106e24daf014848837814c5a8dec
  • Codon count by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/30
  • Updated logo by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/25
  • Random DNA generator script by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/26/commits/1193dc014b6c31ad69b781a02447ddff5dd62696
  • Timing code (and gitignore) by @Nv7-GitHub in https://github.com/Verisimilitude11/DNAnalyzer/pull/26/commits/bc86e34ce940c53c2cf15e3e06b22a2ef0c1ef9d
  • Merge by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/26
  • Merge by @Verisimilitude11 in https://github.com/Verisimilitude11/DNAnalyzer/pull/27
  • [ImgBot] Optimize images by @imgbot in https://github.com/Verisimilitude11/DNAnalyzer/pull/31

New Contributors

  • @Nv7-GitHub made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/26
  • @imgbot made their first contribution in https://github.com/Verisimilitude11/DNAnalyzer/pull/31

Known Issues

  • Gene(s) with the highest coverage doesn't work as expected in https://github.com/Verisimilitude11/DNAnalyzer/issues/11

How to download

  1. Download and extract DNAnalyzer.jar / DNAnalyzer.rar / DNAnalyzer.zip
  2. Open the extracted folder through an IDE
  3. Make sure that you have JDK 11 or above
  4. Run Main.java which can be found under the files folder

Full Changelog: https://github.com/Verisimilitude11/DNAnalyzer/compare/v1.1.0...v1.2.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing Reduced External Dependencies

What's Changed

  • Create dependabot.yml in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/14
  • Create codeql.yml in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/15
  • Create maven.yml in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/16
  • Delete ideas.txt in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/20
  • Removed all dependencies on the Duke Software Library as it wasn't fully compatible in #22

Known Issues

  • #11
  • FASTA file compatibility isn't fully tested in this build as it shifted to directly using a StringBuilder from a StorageResource.

How to download

  1. Download and extract Algorithm-for-Analyzing-Genes-in-DNA.zip
  2. Open the extracted folder through an IDE
  3. Make sure that you have JDK 11 or above
  4. Run entrypoint.java which can be found under the files folder

Full Changelog: https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/compare/v1.0.0...v1.1.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing FASTA File Compatibility

What's Changed

  • Update README.md to add citations and more content by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/4
  • Create CODEOFCONDUCT.md by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/5
  • Create LICENSE by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/6
  • Added issue templates by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/7
  • StorageResource and FASTA file compatibility check by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/9

Improvements

This release introduces the capability to parse .fa (FASTA files). In bioinformatics, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.

How to download

  1. Download and extract files.jar and docs.zip
  2. Open the extracted folder through an IDE
  3. Make sure that you have JDK 11 or above
  4. Run entrypoint.java

Full Changelog: https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/compare/v1.0.0-beta.0...v1.0.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing First Stop Codon Only

What's Changed

  • Create README.md by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/1
  • Finds first stop codon only. by @Verisimilitude11 in https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/pull/3

Full Changelog: https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/compare/v1.0.0-alpha.2...v1.0.0-beta.0

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Introducing a Refactored Algorithm

Improvements

Through refactoring, this release significantly improves code readability. Furthermore, the algorithm has been greatly improved, and the code will soon be released from alpha. In the near future, I intend to incorporate machine learning to improve the user experience.

Two ways to run the application

  1. Download and extract only the .jar file
  2. Download and run all four .java files with entryPoint.java as the main class. If all of the .java files are not in the same folder, it will not run.

Full Changelog

https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/commits/v1.0.0-alpha.2

- HTML
Published by VerisimilitudeX over 3 years ago

dnanalyzer - Simple Algorithm (ATG-TAA)

Simple algorithm for detecting genes with start codon 'ATG' and stop codon 'TAA'. I will be adding more start and stop codons as well as the other features described in future releases. Run Part1.java in any IDE (I used Visual Studio Code and BlueJ for testing).

Full Changelog: https://github.com/Verisimilitude11/Algorithm-for-Analyzing-Genes-in-DNA/commits/v1.0.0-alpha.0

- HTML
Published by VerisimilitudeX over 3 years ago