Bio-Informatics Software

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Bio-Informatics Software

  • Take Advantage of O365 + Online Backup Bundles Take Advantage of O365 + Online Backup Bundles Icon
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  • Want to improve your MSP’s revenue? Price your services right. Want to improve your MSP’s revenue? Price your services right. Icon
    Want to improve your MSP’s revenue? Price your services right. Icon

    Get the ebook, The Managed Services Pricing Guide 2.0 to get industry best practices on pricing managed services.

    You choose software for your IT business so it makes you money. The margins must be good enough to justify the cost. SolarWinds RMM was priced to give you the margins you need to earn a healthy amount of monthly recurring revenue. Download our all-new Managed Services Pricing Guide 2.0 to find what revenue to expect for your services, including light monitoring, web protection, patching management, backup and more.
  • Behavioral Monitoring Tool

    Used to record and analyze some behavioural experiments in neuroscience (using usb webcam). it was developed in collaboration with neuropharmacology lab at Faculty of Medicine, Ain Shams University. it can use(JMF,OpenCV,JMyron & AGCamLib) for webcam

    Downloads: 22 This Week Last Update: See Project
  • TGI Clustering Tool Icon

    TGI Clustering Tool

    A software solution for clustering large EST/mRNAs datasets.

    Downloads: 22 This Week Last Update: See Project
  • Biological Pathway Exchange Language

    A Data Exchange Format for Biological Pathway Information

    BioPAX is a standard language for integration, exchange, visualization and analysis of biological pathway data. BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

  • BioWord Icon

    BioWord

    A Microsoft Word add-in for biological sequence manipulation

    BioWord, a Microsoft Word add-in, allows instant access to most sequence manipulation needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery.

  • RDXplorer

    The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.

  • Take Our Survey. We Plant a Tree. Take Our Survey. We Plant a Tree. Icon
    Take Our Survey. We Plant a Tree. Icon

    In honor of Earth Day, HPCC Systems is committed to planting 10,000 new trees across our national forests.

    HPCC Systems is dedicated to the environment and is giving you the opportunity to take action and be a small part of a big impact. In partnership with the National Forest Foundation, HPCC Systems is growing and promoting awareness of environmental sustainability with their 10K Trees Challenge. The best time to plan a tree was 20 years ago. The second best time is now! Take our survey and take part in helping the environment.
  • QIIME

    The QIIME project has moved to GitHub. You can now find us at http://github.com/qiime/. As always, you can find the QIIME website at http://www.qiime.org.

  • EXCAVATOR2tool

    Enhanced tool for detecting CNVs from whole-exome sequencing data

    ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!!ATTENTION!!!!! We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies. EXCAVATO2 paper: http://nar.oxfordjournals.org/content/early/2016/08/09/nar.gkw695.full?keytype=ref&ijkey=O8r64Qj81gfMzLo

    Downloads: 21 This Week Last Update: See Project
  • Parallel Iterative Deconvolution

    Parallel Iterative Deconvolution is a multithreaded ImageJ plugin for iterative image deblurring.

    Downloads: 21 This Week Last Update: See Project
  • BioC

    We describe a simple XML format to share text documents and annotation

    A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining.

    Downloads: 20 This Week Last Update: See Project
  • Linking Yabi with RDA

    This software system enables publication of YABI workflows to the RDA.

    Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror hosted at the University of Queensland. With the support of ANDS, QFAB has developed this software system to enable the publication of services and collections based of Yabi workflows and datasets. By sharing the description of their workflows, scientists facilitate the diffusion and re-use of their data. This website provides access to the workflows and datasets that have been made public. By login in, scientist can edit, manage and publish their collection descriptions to the Research Data Australia.

    Downloads: 20 This Week Last Update: See Project
  • Get the Edge; Toad Edge Get the Edge; Toad Edge Icon
    Get the Edge; Toad Edge Icon

    Your next-gen toolset for MySQL database environments

    If your organization takes advantage of the cost-effective, flexible MySQL open source database platform, then you need a toolset that supports your commitment to open source relational databases.  Toad Edge for MySQL has what you need and helps you ramp up on MySQL quickly, ensuring faster time to value.
  • SeqHunter2 Icon

    SeqHunter2

    a stand-alone bioinformatics software for querying genome sequences

    SeqHunter2 is a stand-alone software with graphical user interface, running on Microsoft windows system. It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link to the website. The full version collects all available oomycete plant pathogens genome sequences and information of research related resource, while the lite version is flexible for non-oomycete users to collected the data they are interested.

    Downloads: 20 This Week Last Update: See Project
  • GMDR

    A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

  • DIA-Umpire Icon

    DIA-Umpire

    Computational analysis pipeline for DIA proteomics data

    Computational package for identification and quantitation analysis of mass spectrometry-based proteomics data using data independent acquisition (DIA)

  • FSA

    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

  • MicroRNA Discovery By Deep Sequencing

    MIREAP is a tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

  • proTRAC Icon

    proTRAC

    Use proTRAC to annotate genomic piRNA clusters

    proTRAC detects genomic piRNA clusters. It considers all the relevant features of mapped sequence reads like the amount of 1U/10A, size and strand bias to ensure a high specificity.

  • BEDTools

    BEDTools is a suite of utilities for comparing genomic features in BED format. These utilities allow one to quickly address tasks such as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps.

    Downloads: 19 This Week Last Update: See Project
  • DockoMatic

    DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

    Downloads: 19 This Week Last Update: See Project
  • Hamlib

    A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8

    Downloads: 19 This Week Last Update: See Project
  • MToolBox

    A bioinformatics pipeline to analyze mtDNA from NGS data

    MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php

    Downloads: 19 This Week Last Update: See Project
  • Niche Analyst

    Niche Analyst (NicheA) was developed based on the BAM framework which allows users to create virtual spaces and virtual species, and to analyze ecological niches in both multivariate environmental and geographic spaces, linking views of the niche in the two spaces. The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological niches. NicheA can display ecological niches; calculate their shape, density, location, and other attributes; and quantify similarity among multiple niches.

    Downloads: 19 This Week Last Update: See Project
  • sourcesinc

    Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc

    Downloads: 19 This Week Last Update: See Project
  • Face Detect (JavaCV)

    Face Detection and Facial Feature Extraction using JavaCV

    A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition.

  • GNAT Icon

    GNAT

    GNAT recognizes gene names in text and maps them to NCBI Entrez Gene

    GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.

    Downloads: 18 This Week Last Update: See Project
  • Nemo

    Individual-based forward-time genetics simulation software

    Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework.

    Downloads: 18 This Week Last Update: See Project

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