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  1. 3521
    “…Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. …”
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    CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce
  2. 3522
    por Pissis, Solon P
    Publicado 2014
    “…CONCLUSIONS: Use of MoTeX-II in biological frameworks may enable deriving reliable and important information since real full-length datasets can now be processed with almost any set of input parameters for both single and structured motif extraction in a reasonable amount of time. The open-source code of MoTeX-II is freely available at http://www.inf.kcl.ac.uk/research/projects/motex/.…”
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    MoTeX-II: structured MoTif eXtraction from large-scale datasets
  3. 3523
    “…ReNE can be freely installed from the Cytoscape App Store (http://apps.cytoscape.org/apps/rene) and the full source code is freely available for download through a SVN repository accessible at http://www.sysbio.polito.it/tools_svn/BioInformatics/Rene/releases/. …”
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    ReNE: A Cytoscape Plugin for Regulatory Network Enhancement
  4. 3524
    por Dixit, Abhishek, Dobson, Richard J B
    Publicado 2014
    “…A video tutorial demonstrating the application setup, datasource configuration, and search features is available on YouTube. The application source code is available at the GitHub website and the users are encouraged to suggest new features and contribute to the development of APIs for new EAV systems.…”
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    CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas
  5. 3525
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    Using the value of Lin’s concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images
  6. 3526
    “…We were also able to show the potential of IPO to increase the reliability of metabolomics data. The source code is implemented in R, tested on Linux and Windows and it is freely available for download at https://github.com/glibiseller/IPO. …”
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    IPO: a tool for automated optimization of XCMS parameters
  7. 3527
    “…AVAILABILITY: EmOntoTag can be seen at http://www.bioontology.ch/emontotag; source code can be downloaded from http://emotion-ontology.googlecode.com/svn/trunk/apps/emontotag/and the ontology is available at http://purl.obolibrary.org/obo/MFOEM.owl. …”
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    Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference
  8. 3528
    “…AVAILABILITY AND IMPLEMENTATION: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. …”
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    MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
  9. 3529
    “…PathRings is available free at http://raven.anr.udel.edu/~sunliang/PathRings and the source code is hosted on Github: https://github.com/ivcl/PathRings. …”
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    PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways
  10. 3530
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    Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment
  11. 3531
    “…Consequently, our method is useful in accelerating the applications that require optimal local alignments scores for the same species. The source code is available for download from http://www-hagi.ist.osaka-u.ac.jp/research/code/.…”
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    Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences
  12. 3532
    por Wu, Steven H., Rodrigo, Allen G.
    Publicado 2015
    “…This allows us to perform the analysis on NGS datasets with large numbers of short read fragments. The source code for ABC-MCMC is available at https://github.com/stevenhwu/SF-ABC.…”
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    Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals
  13. 3533
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    FlexDM: Simple, parallel and fault-tolerant data mining using WEKA
  14. 3534
    “…However, since genetic material carries genetic information, the “source code” of all living activities, it is actually reasonable to question the plausibility of such a “revolutionary” transition. …”
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    The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover
  15. 3535
    “…Availability and implementation: The anonymized data collected from the survey and the Matlab source code for data processing can be found at: https://github.com/alexandrovteam/IMS_quality. …”
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    Using collective expert judgements to evaluate quality measures of mass spectrometry images
  16. 3536
    “…The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. …”
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    EHDViz: clinical dashboard development using open-source technologies
  17. 3537
    “…AVAILABILITY: The data and source code for this work are available at: http://bionlp-www.utu.fi/trigger-clustering/. …”
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    Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification
  18. 3538
    “…We also evaluate the diagnostic utility of AWoL-MRF by analyzing the volume differences per disease category in the ADNI1: Complete Screening dataset. We have made the source code for AWoL-MRF public at: https://github.com/CobraLab/AWoL-MRF.…”
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    Manual-Protocol Inspired Technique for Improving Automated MR Image Segmentation during Label Fusion
  19. 3539
    “…We also show that EpiTracer is not sensitive to minor changes in the network. The source code for EpiTracer is provided at Github (https://github.com/narmada26/EpiTracer).…”
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    EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks
  20. 3540
    “…Other ongoing projects using OBCS for statistical data processing are also discussed. The OBCS source code and documentation are available at: https://github.com/obcs/obcs. …”
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    The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis
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