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  1. 2401
    “…The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance levels to define OTUs. The source code is available at http://plaza.ufl.edu/xywang/Mpick.htm.…”
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    M-pick, a modularity-based method for OTU picking of 16S rRNA sequences
  2. 2402
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    MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads
  3. 2403
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    SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies
  4. 2404
    por Dornseifer, Simon, Sczakiel, Georg
    Publicado 2013
    “…The software tool, dubbed RNAslider, is built on the theoretical RNA structure prediction algorithm Mfold. Source code and sample data sets are available on demand. …”
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    Computational identification of biologically functional non-hairpin GC-helices in human Argonaute mRNA
  5. 2405
    “…CNV_SS gave also much more effective results than the conventional methods in the evaluation of FNR, at 3.82% at least and 76.97% at most even when the coverage level of read data is low. CNV_SS source code is freely available from http://dblab.hallym.ac.kr/CNV SS/.…”
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    A computational method for detecting copy number variations using scale-space filtering
  6. 2406
    “…We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby). Availability: The source code of libSBMLSim is available from http://fun.bio.keio.ac.jp/software/libsbmlsim/. …”
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    LibSBMLSim: a reference implementation of fully functional SBML simulator
  7. 2407
    “…Detailed and stringent tests for model performance were carried out, and standardised model description and open access to the source code were provided to open development of the skylark model to others. …”
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    Modelling Skylarks (Alauda arvensis) to Predict Impacts of Changes in Land Management and Policy: Development and Testing of an Agent-Based Model
  8. 2408
    “…All the results and source code are available at http://compbio.cs.umn.edu/NetPathID/.…”
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    Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers
  9. 2409
    “…The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. …”
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    The systems biology simulation core algorithm
  10. 2410
    por Porter, Michael S., Beiko, Robert G.
    Publicado 2013
    “…Conclusions: By using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches. Availability: C++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER. …”
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    SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles
  11. 2411
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    GenePattern flow cytometry suite
  12. 2412
    “…AVAILABILITY AND IMPLEMENTATION: Java source code, binaries and setup instructions are freely available at http://genomes.sapac.edu.au/text_mining/pos_tagger.zip.…”
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    Improved Part-of-Speech Prediction in Suffix Analysis
  13. 2413
    “…These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation. Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/.…”
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    Can Inferred Provenance and Its Visualisation Be Used to Detect Erroneous Annotation? A Case Study Using UniProtKB
  14. 2414
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    CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation
  15. 2415
    “…Additionally, our model provides new insights into the established and widely used Sanger sequencing technology. The source code of our method is made available at http://bioinf.mpi-inf.mpg.de/publications/beggel/linkageinformation.zip.…”
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    Inferring Short-Range Linkage Information from Sequencing Chromatograms
  16. 2416
    “…Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET), as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/.…”
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    BOBA FRET: Bootstrap-Based Analysis of Single-Molecule FRET Data
  17. 2417
    por Gautier, Laurent, Lund, Ole
    Publicado 2013
    “…A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.…”
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    Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads
  18. 2418
    “…We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. …”
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    Rapid Reconstruction of 3D Neuronal Morphology from Light Microscopy Images with Augmented Rayburst Sampling
  19. 2419
    “…For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.…”
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    CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
  20. 2420
    “…Our DiME compiled software, R/C++ source code, sample data and a tutorial are available at http://www.cs.bham.ac.uk/~szh/DiME.…”
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    DiME: A Scalable Disease Module Identification Algorithm with Application to Glioma Progression
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