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  1. 3001
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    Symmetrical treatment of “Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition”, for major depressive disorders
  2. 3002
    “…CONCLUSIONS: Our analysis show that the proposed data integration strategy is able to improve the quality of the predicted interactions, and can speed up the identification of new drug-target interactions as well as identify relevant information for the task. AVAILABILITY: The source code and data sets are available at www.cin.ufpe.br/~acan/kronrlsmkl/. …”
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    A multiple kernel learning algorithm for drug-target interaction prediction
  3. 3003
    “…Availability and implementation: C [Formula: see text] source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/. …”
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    MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues
  4. 3004
    “…In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp.…”
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    A deep learning framework for modeling structural features of RNA-binding protein targets
  5. 3005
    “…BACKGROUND: In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possible nucleotide substitution models in the Maximum Likelihood (ML) setting under the common Akaike, corrected Akaike, and Bayesian information criteria. …”
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    Does the choice of nucleotide substitution models matter topologically?
  6. 3006
    “…The ME corpus, test corpus, source code, and virtual machine image with pre-configured software are available at www.sbi.kmutt.ac.th/ preecha/metrecon.…”
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    An integrated text mining framework for metabolic interaction network reconstruction
  7. 3007
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    A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes
  8. 3008
    “…We demonstrated this framework in a search for prognostic biomarkers in breast cancer which resulted in the identification of several prognostic image features and a promising multimodal (imaging and genomic) prognostic signature. The source code for the image analysis procedures is freely available. …”
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    Joint analysis of histopathology image features and gene expression in breast cancer
  9. 3009
    “…CONCLUSIONS: Our results suggest that computational sample stratification selects potentially sensitive samples for targeted therapies and can aid in precision medicine drug repositioning. Source code is available from http://csblcanges.fimm.fi/GOPredict/. …”
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    Data integration to prioritize drugs using genomics and curated data
  10. 3010
    “…The web server including source code and the datasets are available at http://219.219.62.123:8888/ppi_ab/.…”
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    RVMAB: Using the Relevance Vector Machine Model Combined with Average Blocks to Predict the Interactions of Proteins from Protein Sequences
  11. 3011
    “…We therefore conclude that it is vital that future economic models in chronic pain are designed to be fully transparent and hope our open-source code is useful in order to aspire to a common approach to modelling pain that includes robust sensitivity analyses to test structural and parameter uncertainty. …”
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    Economic evaluation in chronic pain: a systematic review and de novo flexible economic model
  12. 3012
    “…Availability and Implementation: The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF. …”
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    BioASF: a framework for automatically generating executable pathway models specified in BioPAX
  13. 3013
    por Liu, Bo, Zhu, Dixian, Wang, Yadong
    Publicado 2016
    “…Availability and implementation: deBWT is implemented in C language, the source code is available at https://github.com/hitbc/deBWT or https://github.com/DixianZhu/deBWT Contact: ydwang@hit.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    deBWT: parallel construction of Burrows–Wheeler Transform for large collection of genomes with de Bruijn-branch encoding
  14. 3014
    “…Availability and implementation: Documentation and source code for Alpha-CENTAURI are freely available at http://github.com/volkansevim/alpha-CENTAURI. …”
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    Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
  15. 3015
    “…Availability and implementation: Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads. …”
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    repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
  16. 3016
    “…CONCLUSIONS: The computational toolkit, spektr, has been updated to version 3.0, validated against measurements and existing models, and made available as open source code. Video tutorials for the spektr function library, UI, and optimization tool are available.…”
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    Technical Note: spektr 3.0—A computational tool for x-ray spectrum modeling and analysis
  17. 3017
    “…The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR, or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR. …”
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    RevEcoR: an R package for the reverse ecology analysis of microbiomes
  18. 3018
    “…Availability and Implementation: A MATLAB implementation is provided within the freely available, open-source modeling environment Data2Dynamics. Source code for all examples is provided online at http://www.data2dynamics.org/. …”
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    L(1) regularization facilitates detection of cell type-specific parameters in dynamical systems
  19. 3019
    “…Availability and Implementation: pong is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong. …”
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    pong: fast analysis and visualization of latent clusters in population genetic data
  20. 3020
    “…IDGenerator is freeware under the GNU General Public License version 3; a Windows port and the source code can be downloaded at the Open Science Framework website: https://osf.io/urs2g/.…”
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    IDGenerator: unique identifier generator for epidemiologic or clinical studies
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