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  1. 1241
    por Xiong, Yi, Xia, Junfeng, Zhang, Wen, Liu, Juan
    Publicado 2011
    “…Furthermore, a brief case study suggests that the weighted average features are powerful for identifying DNA-binding residues and are promising for further study of protein structure-function relationship. The source code and datasets are available upon request.…”
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    Exploiting a Reduced Set of Weighted Average Features to Improve Prediction of DNA-Binding Residues from 3D Structures
  2. 1242
    “…A web-based service as well the source code are provided freely at http://srvgen.upct.es/efficiency.html under the GPL v2 license.…”
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    pcrEfficiency: a Web tool for PCR amplification efficiency prediction
  3. 1243
    “…IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.…”
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    The IntAct molecular interaction database in 2012
  4. 1244
    “…GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request.…”
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    GONUTS: the Gene Ontology Normal Usage Tracking System
  5. 1245
    “…IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.…”
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    IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface
  6. 1246
    por Kehr, Birte, Weese, David, Reinert, Knut
    Publicado 2011
    “…Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.…”
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    STELLAR: fast and exact local alignments
  7. 1247
    “…ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively. Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela. …”
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    ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites
  8. 1248
    “…An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. …”
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    xQTL workbench: a scalable web environment for multi-level QTL analysis
  9. 1249
    “…Availability and implementation: Source code is available at: http://bmi.bmt.tue.nl/sysbio/software/pua.html Contact: j.vanlier@tue.nl; N.A.W.v.Riel@tue.nl Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    A Bayesian approach to targeted experiment design
  10. 1250
    por Zabet, Nicolae Radu, Adryan, Boris
    Publicado 2012
    “…Availability: http://logic.sysbiol.cam.ac.uk/grip, program and source code Contact: n.r.zabet@gen.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    GRiP: a computational tool to simulate transcription factor binding in prokaryotes
  11. 1251
    “…For non-sequential alignment problems, SAS-Pro leads to alignments with high degree of similarity with known reference alignments. The source code of SAS-Pro is available for download at http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html.…”
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    SAS-Pro: Simultaneous Residue Assignment and Structure Superposition for Protein Structure Alignment
  12. 1252
    “…CONCLUSIONS: Experimental results on RNA-Seq data generated from blood cell tissue of three Hapmap individuals show that our methods yield increased accuracy compared to several widely used methods. The open source code implementing our methods, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/NGSTools/.…”
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    Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data
  13. 1253
    “…Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. …”
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    Software support for SBGN maps: SBGN-ML and LibSBGN
  14. 1254
    “…Application to the Cancer Genome Atlas glioblastoma, ovarian and lung squamous cancer datasets revealed several novel mutations with predicted high impact including several genes mutated at low frequency suggesting the approach will be complementary to current approaches that rely on the prevalence of events to reach statistical significance. Availability: All source code is available at the github repository http:github.org/paradigmshift. …”
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    PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
  15. 1255
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    Automatic Fortran to C++ conversion with FABLE
  16. 1256
    “…It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. …”
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    ACPYPE - AnteChamber PYthon Parser interfacE
  17. 1257
    por Frampton, Matthew, Houlston, Richard
    Publicado 2012
    “…ArtificialFastqGenerator was released in January 2012. Source code, example files and binaries are freely available under the terms of the GNU General Public License v3.0. from https://sourceforge.net/projects/artfastqgen/.…”
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    Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
  18. 1258
    por Schreyer, Adrian M, Blundell, Tom
    Publicado 2012
    “…Online chemical databases that offer a shape-based similarity method might also find advantage in using USRCAT due to its accuracy and performance. The source code is freely available and can easily be modified to fit specific needs.…”
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    USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints
  19. 1259
    “…Given its accuracy, speed, and simplicity, TreeFix should be applicable to a wide range of analyses and have many important implications for future investigations of gene evolution. The source code and a sample data set are available at http://compbio.mit.edu/treefix.…”
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    TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
  20. 1260
    “…Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. …”
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    Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
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