SIGs/SciTech/BioinformaticsWishList

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* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment ([https://bugzilla.redhat.com/show_bug.cgi?id=597315 Review Request])
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* [http://autodock.scripps.edu/ Autodock] - Suite of automated molecular docking tools
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* [http://vina.scripps.edu/ Autodock Vina] - Tool for drug discovery, molecular docking and virtual screening
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* [http://copasi.org/ COPASI] - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
 
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
 
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
 
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing ([https://bugzilla.redhat.com/show_bug.cgi?id=597307 Review Request])
 
 
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
 
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
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* [http://www.broadinstitute.org/igv/ Integrative Genomics Viewer] - java-based graphical genomics viewer (licensed under GPLv2)
 
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
 
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools] - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
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* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools] - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
 
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML NCBI C Toolkit ] - NCBI libraries and tools for biology applications [http://www.environnement.ens.fr/perso/dumas/fc-srpms/ncbi-6.1.20081116a-1.fc10.src.rpm srpm here]
 
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML NCBI C Toolkit ] - NCBI libraries and tools for biology applications [http://www.environnement.ens.fr/perso/dumas/fc-srpms/ncbi-6.1.20081116a-1.fc10.src.rpm srpm here]
 
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology  
 
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology  
 
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
 
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
* <strike>[http://samtools.sourceforge.net/ SAMtools] - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.</strike>
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* [http://staden.sourceforge.net/ Staden] - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
* [http://staden.sourceforge.net/ Staden] - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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* [http://www.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.
 
* [http://www.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.
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* [http://www.physionet.org/physiotools/wfdb.shtml The WFDB Software Package] - Software for viewing, analyzing, and creating recordings of physiologic signals
  
 
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Revision as of 18:34, 6 December 2012

  • Autodock - Suite of automated molecular docking tools
  • Autodock Vina - Tool for drug discovery, molecular docking and virtual screening
  • COPASI - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
  • Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
  • GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
  • Integrative Genomics Viewer - java-based graphical genomics viewer (licensed under GPLv2)
  • MIRA - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
  • NCBI BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
  • NCBI C Toolkit - NCBI libraries and tools for biology applications srpm here
  • NCBI C++ Toolkit - a new generation of NCBI libraries and tools for biology
  • pyQPCR - qPCR analysis tool
  • Staden - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
  • Taverna - Tool for automation of experimental workflows.
  • The WFDB Software Package - Software for viewing, analyzing, and creating recordings of physiologic signals