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  1. 2961
    “…This highlights the physical non-viability of the fisa decoy set, and possible issues in benchmarking other methods using this set. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134.…”
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    Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms
  2. 2962
    “…The algorithm is available as a web-demo at http://fich.unl.edu.ar/sinc/web-demo/bsom-lite/. The source code and the data sets supporting the results of this article are available at http://sourceforge.net/projects/sourcesinc/files/bsom.…”
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    Improving clustering with metabolic pathway data
  3. 2963
    “…CONCLUSION: SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.…”
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    SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines
  4. 2964
    “…Another advantage of our methods arises from the explicit feature space representation, which can be used to analyze the characteristic features of protein families. The source code of SVM-DT and SVM-DR is available at http://bioinformatics.hitsz.edu.cn/DistanceSVM/index.jsp…”
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    Using distances between Top-n-gram and residue pairs for protein remote homology detection
  5. 2965
    “…We also validate the novelty of predictions by evaluating the method on recently reported OMIM associations and on associations recently reported in the literature. Availability: Source code and datasets can be downloaded from http://bigdata.ices.utexas.edu/project/gene-disease. …”
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    Inductive matrix completion for predicting gene–disease associations
  6. 2966
    “…Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html. …”
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    An efficient parallel algorithm for accelerating computational protein design
  7. 2967
    “…The superior performance of capDSD in this context confirms that treating the pathways as probabilistic units is more powerful than simply incorporating pathway edges independently into the network. Availability: All source code for calculating the confidences, for extracting pathway information from KEGG XML files, and for calculating the cDSD, caDSD and capDSD matrices are available from http://dsd.cs.tufts.edu/capdsd Contact: lenore.cowen@tufts.edu or benjamin.hescott@tufts.edu Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
  8. 2968
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    Methylation plotter: a web tool for dynamic visualization of DNA methylation data
  9. 2969
    por Stojmirović, Aleksandar, Yu, Yi-Kuo
    Publicado 2014
    “…The input data, final results and the source code are available at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/ProteinComplexDAG/.…”
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    Building a Hierarchical Organization of Protein Complexes Out of Protein Association Data
  10. 2970
    “…CONCLUSIONS: SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.…”
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    SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models
  11. 2971
    “…Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox. …”
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    PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
  12. 2972
    “…CONCLUSIONS: Based on our results, we conclude that morFeus is a powerful and specific search method for detecting remotely conserved orthologs. morFeus is freely available at http://bio.biochem.mpg.de/morfeus/. Its source code is available from Sourceforge.net (https://sourceforge.net/p/morfeus/). …”
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    morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring
  13. 2973
    por Capra, John A., Kostka, Dennis
    Publicado 2014
    “…Availability and implementation: Source code is available at www.kostkalab.net/software. …”
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    Modeling DNA methylation dynamics with approaches from phylogenetics
  14. 2974
    “…Availability and implementation: Source Code implementing the method is available at: http://research.ics.aalto.fi/mi/software/GFAsparse Contact: suleiman.khan@aalto.fi or samuel.kaski@aalto.fi Supplementary Information: Supplementary data are available at Bioinformatics online.…”
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    Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis
  15. 2975
    “…ADTEx is implemented as a user friendly software package using Python and R statistical language. Source code and sample data are freely available under GNU license (GPLv3) at http://adtex.sourceforge.net/. …”
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    Inferring copy number and genotype in tumour exome data
  16. 2976
    “…Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.…”
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    The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data
  17. 2977
    “…The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/. …”
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    Integrating protein structural dynamics and evolutionary analysis with Bio3D
  18. 2978
    “…CONCLUSIONS: We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.…”
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    A Fuzzy-Match Search Engine for Physician Directories
  19. 2979
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    Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments
  20. 2980
    “…Experimental results, using real and synthetic data, show that this implementation outperforms the one by Pinho et al. The open-source code of our implementation is freely available at http://github.com/solonas13/maw. …”
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    Linear-time computation of minimal absent words using suffix array
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