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Free Open Source Bio-Informatics Software

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Bio-Informatics Software

  • Find out what (or who) is slowing down your network Icon
    Find out what (or who) is slowing down your network Icon

    Get comprehensive network bandwidth analysis and performance monitoring with SolarWinds® Bandwidth Analyzer Pack.

    Network slow, but you don't know the cause? Use Bandwidth Analyzer Pack (BAP) to monitor and analyze network bandwidth performance and traffic patterns. With BAP, you can identify which users, applications, and protocols are consuming the most bandwidth. You can also monitor Wireless LAN Controller traffic to see what applications and clients are using your wireless network. Try it free for 30 days!
  • SolarWinds is #1 in Network Monitoring. Icon
    SolarWinds is #1 in Network Monitoring. Icon

    Reduce network outages and improve performance with advanced network monitoring software

    SolarWinds® Network Performance Monitor (NPM) is the ONLY monitoring solution with NetPath™ for hop-by-hop visibility into your critical paths, on-premises and into the cloud. NPM also features PerfStack™, helping you accelerate identification of root cause by dragging-and-dropping network performance metrics on a common timeline for immediate visual correlation across all of your network data. See why we're the leader. Try it free for 30 days!
  • SAM tools

    SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools

  • Bowtie

    Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

  • Jmol Icon

    Jmol

    An interactive viewer for three-dimensional chemical structures.

    Over 10,000,000 page views! Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

  • Burrows-Wheeler Aligner

    BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

  • Gwyddion Icon

    Gwyddion

    Scanning probe microscopy data visualisation and analysis

    A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis.

  • Identify and respond to threats before damage is done Icon
    Identify and respond to threats before damage is done Icon

    A SIEM that makes it easy to use logs for security, compliance, and troubleshooting.

    SolarWinds® Log & Event Manager (LEM) delivers comprehensive Security Information and Event Management (SIEM) capabilities in a highly affordable, easy-to-use, and quick-to-deploy virtual appliance. LEM provides the visibility, security, and control that IT professionals need to alert on and respond to security threats, and assist in meeting the regulatory compliance guidelines of HIPAA, PCI DSS, SOX, and more. Try it FREE for 30 days!
  • MeV

    Please use WebMeV for all NGS and Microarray analysis: http://mev.tm4.org/

  • Primer3 - PCR primer design tool

    Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.

  • Java Treeview

    Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format

  • Systems Biology Markup Language (SBML) Icon

    Systems Biology Markup Language (SBML)

    A file format for exchanging computational models in systems biology

    The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

  • MUMmer

    MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

  • REST Debugger - Explore. Understand. Integrate Icon
    REST Debugger - Explore. Understand. Integrate Icon

    Embarcadero's free solution for exploring, understanding and integrating RESTful web services with Delphi and C++Builder apps.

    Explore and Understand RESTful Web Services The Embarcadero REST Debugger empowers developers to explore, test, and ultimately understand how a RESTful web service works. Dive right into REST data with filterable JSON blobs, streamlined OAuth 1.0/2.0 authentication, and configurable request/resource parameters. Give it a try! It's FREE! (no credit card or commitment required)
  • APBS Icon

    APBS

    APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>. Please register at http://goo.gl/LGVU5j before downloading!

  • OpenChrom Icon

    OpenChrom

    OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.

  • vcftools Icon

    vcftools

    A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/

  • OpenClinic GA Icon

    OpenClinic GA

    Open Source Integrated Hospital Information Management System

    OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities.

  • picard

    A set of tools for working with high-throughput sequencing data

    A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team

  • RasMol

    The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

  • VarScan Icon

    VarScan

    Variant detection in next-generation sequencing data

    Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes.

  • OpenMS

    An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++.

  • CARE2X - Integrated Hospital Info System Icon

    CARE2X - Integrated Hospital Info System

    Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab

  • BBMap

    BBMap short read aligner, and other bioinformatic tools.

    This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more!

    Downloads: 436 This Week Last Update: See Project
  • CodonW

    CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.

  • MrBayes Icon

    MrBayes

    MrBayes is a program for the Bayesian estimation of phylogeny. The project has been moved to GitHub: https://github.com/NBISweden/MrBayes

    Downloads: 362 This Week Last Update: See Project
  • Toxtree: Toxic Hazard Estimation Icon

    Toxtree: Toxic Hazard Estimation

    Toxicity prediction for chemical compounds

    A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.

  • AMOS

    AMOS is a collection of tools for genome assembly

    AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

  • MarsBaR ROI toolbox for SPM

    MarsBaR is a matlab toolbox for analyzing image data within Regions of Interest (ROIs).

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