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Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can... -
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code"... -
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PDPBioGen
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of the Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis... -
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PUMA Repository
Pascal Units for Medical Applications
The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers. -
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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Palibino
Pascal library for bioinformatics
Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology. -
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DigiOz .NET Portal
ASP.NET MVC Based Portal CMS System to Create an Instant Website
DigiOz .NET Portal is a FREE web based portal CMS system written in ASP.NET MVC 5 in C# which uses a Microsoft SQL Database to allows webmasters to setup and customize an instant website for either business or personal use. List of Technologies used: - ASP.NET MVC 5 - Microsoft SQL Server - Bootstrap - HTML 5 - jQuery Demo Site: http://digioznetportal.digioz.net/ Source Code: https://sourceforge.net/p/digioznetportal/codenew/ci/master/tree/ Installation Instructions:... -
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Quadric
Application for simple base-2 binary to base-4 DNA-code conversion
Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
... * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
...The program is available in the form of web (link below) and standalone GUI applications. Program source code is also provided.. The web and GUI apps do not require any additional software to run. To install the GUI version, simply download and run the installer for PC or Mac. To install in Linux, follow in-package instructions or visit the VirtualGlycome.org FAQ page. The source code can be edited and run using MATLAB2014b or later. How to Cite: DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information Kai Cheng; Yusen Zhou; Sriram Neelamegham Glycobiology (2017) 27 (3): 200-205 Source code also available at: https://github.com/neel-lab/DrawGlycan-SNFGv2 Abstract & Full Text: https://doi.org/10.1093/glycob/cww115 -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
This repository contains the most updated code version of MANTIS, the Multi-locus ANTIgenic Simulator R-package. MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN... -
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The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
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VirtualDNA
Make your own flowers
virtualDNA is a Processing3 game with an Android APK file in it. You can make your own flowers by crossing a flowerpool. There is a gamelike feature where you have to make a flower that ressembles a given one. -
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Protdraw
Create portable, flexible domain drawings of protein sequences
For ProtDraw to work on MacOS Yosemite, you must install a patched Pert Tk. Go to https://github.com/eserte/perl-tk and click the Download zip button. Run the unzip command, cd to the extracted directory and follow the directions in the 'INSTALL' file (using 'sudo' if necessary). ProtDraw creates flexible, easily-interpretable and portable illustrations of the domain structures of input sequences. ProtDraw is accompanied by makeProtDraw, a helper program which runs hmmer3 on a specified... -
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noise-free-cnv
program for analyzing and manipulating DNA microarray data
CNV calling software may produce false-positive calls due to imperfect source material. Direct inspection of the microarray data with the noise-free-cnv software helps to appreciate the quality of the data and to identify artificial calls. With noise-free-cnv it is possible to visualize individual datasets, to compare different datasets and to perform simple transformations. The visualization and the suppression of genomic waves, the comparison of two datasets by subtraction and the... -
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BioGenie
BioGenie is presented as a complete package for Biological solutions.
Bioinformatics as an emerging research area spreads out many challenges to both the Bioinformaticists and the Bioinformaticians. BioGenie is presented as a complete package for tackling these challenges. Accommodating all three platforms, that is, a desktop application, a web application and a mobile (android-based) application, BioGenie outperforms all existing softwares engineered to assist heavy and complex computations. The GUI is very well-designed guiding the user technically with ease. -
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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
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Easy install web server for Genetic and Molecular Biological Laboratory so that PI can update lab homepage himself. Also serve as Lab database server that store DNAStrider plasmid , order tracking and mouse colony database.
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EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is written in Perl and is exceedingly simple to install, configure, maintain and use.
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