Software for Biohackers

Posted by – July 30, 2009

Some open source software collections of biology interest are noted here. I’ll update this list as time goes on. If you would like to have your project listed too, leave a comment with all the fields of the table and I’ll add your project. If any of these links do not work, let me know too.

Name Status Field Language Description
Eclipse Stable Programming, editing, building, debugging Java, C, C++, Perl, .. Eclipse is the most widely adopted software development environment in terms of language support, corporate support, and user plugin support. It is open source. It’s the “Office” suite for programming.
BioPerl Stable Bioinformatics Perl, C BioPerl has many modules for genomic sequence analysis/matching, genomic searches to databases, file format conversion, etc.
BioPython Stable Bioinformatics Python, C BioPython has many modules for computational biology.
BioJava Stable Bioinformatics Java BioJava has many modules for computational biology.
BioLib Stable Bioinformatics C, C++ BioLib has many modules for file format conversion, integration to other Bio* language projects, genomic sequence matching, etc.
Bio-Linux Stable Operating System with Bundled Bioinformatics Applications Many “A dedicated bioinformatics workstation – install it or run it live”
DNA Linux Stable Operating System with Bundled Bioinformatics Applications Many “DNALinux is a Virtual Machine with bioinformatic software preinstalled.”
Several Synthetic Biology editors, simulators, or suites, listed at OpenWetWare Computational Tools, such as:
Synthetic Biology Software Suite (SynBioSS), BioJADE, GenoCAD, BioStudio, BioCad,TinkerCell, Clotho
Work In Progress Synthetic Biology Moslty Java, some Web based, some Microsoft .NET Pathway modeling & simulation for synthetic biology genetic engineering, editing, parts databases, etc
APE (A Plasmid Editor) Stable Genetic engineering Java DNA sequence and translation editor
If you enjoyed this post, make sure you subscribe to my RSS feed!

8 Comments on Software for Biohackers

  1. Norman says:

    should add this useful tool GENtle to your list:

    description from the website: GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. It is free software under GPL.

    http://gentle.magnusmanske.de/

  2. sung says:

    Someone well versed in handling bioinformatics software should do some comprehensive review on the softwares listed in OpenWetWare Computation Tools page. Lot of those packages overlap, and with no explanation about the software packages on the website their educational value is nil.

  3. Cobra Toolbox
    http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox

    The COnstraint-Based Reconstruction and Analysis Toolbox for Matlab includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models. The Cobra toolbox will work with version 2.0 of the SBML toolbox.

    COBRA Toolbox v1.3.3 features

    * Reading and writing models in SBML format
    *

    Reading models exported from the SimPheny program from Genomatica
    * Changing model content and parameters: reactions, bounds, objectives, gene associations
    *

    Network and flux distribution output to Cytoscape
    * Common interfaces to a number of free and commercial linear programming solvers
    * Flux balance analysis, linear MOMA, and standard quadratic MOMA analysis
    * Robustness and double robustness analysis
    * Single and double gene deletion analysis
    * Dynamic flux balance analysis (batch culture simulation)
    * Flux variability analysis
    * Uniform sampling of flux space using artificial centering hit-and run
    * Tools for statistical analysis of flux samples
    * Finding correlated reaction sets
    * Reporter metabolite analysis

  4. http://cadnano.org/

    caDNAno is software for design of three-dimensional
    DNA origami nanostructures. It was written with the goal of providing a simple and user-friendly interface to facilitate a process that can be complex and error-prone.
    caDNAno features:

    * No programming required
    * Integrated 2D and 3D interfaces
    * Visual cues to aid design process
    * Export formats: SVG, X3D, JSON
    * Platform independent
    * Open source (MIT license)

  5. http://sysbio.di.uminho.pt/anote/wiki/index.php/Welcome

    @Note is a Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. In fact, it aims to provide support to three different usage roles: biologists, text miners and application developers.

    The major guidelines of its development were interoperability, extensibility and user-friendly interface. The workbench is meant for both BioTM research and curation. On one hand, it supports regular curation activities, providing an intuitive Graphical User Interface (GUI) interface that does not require any knowledge about workbench or technique implementation. On the other hand, it is also meant for people with programming skills that might wish to extend the workbench capabilities.

    @Note is implemented over AIBench[1], a JAVA framework meant to ease the development of Artificial Intelligence and Data Analysis applications. The main strengths of AIBench are its clear design and available services. Its design is problem-independent, minimum framework-related code is required in order to produce new functionalities. Moreover, it generates GUI code and enforces well-designed MVC code, supporting three main artifacts: operations, data types and views. Operations and data types are used in problem modelling while views display data in a “friendly” way.

    Regarding operations, @Note sustains the general workflow of BioTM, fully covering all activities performed in manual curation. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.

  6. Several projects w/ source code can be found here with formal publication: Source Code for Biology and Medicine. All aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining. http://www.scfbm.org/

    One particular project:

    Paper: A Perl toolkit for LIMS development. Source Code for Biology and Medicine 2008, 3:4 doi:10.1186/1751-0473-3-4 http://www.scfbm.org/content/3/1/4

    ArrayPipeline http://sourceforge.net/projects/arraypipeline/
    by chris_trl, james_morris81

    ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines

  7. For a selection of phylogenetic tools on Mac OS/X, Windows and Unix, visit the University of North Carolina at Chapel Hill, Center for Bioinformatics software tools page: http://bioinformatics.unc.edu/software/opensource/index.htm.

  8. PerlPrimer – open-source PCR primer design
    http://perlprimer.sourceforge.net

    PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design. PerlPrimer is written in Perl and Perl/Tk.

    PerlPrimer’s current features include the following:

    * Calculation of possible primer-dimers
    * Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
    * Ability to BLAST search primers using the NCBI server or a local server
    * Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
    * ORF and CpG island detection algorithms
    * Ability to add cloning sequences to primers, automatically adjusted to be in-frame
    * QPCR primer design without manual intron-exon boundary entry