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  1. 1201
    por Wilczyński, Bartek, Dojer, Norbert
    Publicado 2009
    “…Besides the availability of the standalone application and the source code, we have developed a web interface to BNFinder application running on our servers. …”
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    BNFinder: exact and efficient method for learning Bayesian networks
  2. 1202
    “…The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.…”
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    Fast Statistical Alignment
  3. 1203
    por Guo, Xin, Hartemink, Alexander J.
    Publicado 2009
    “…Availability: Supplementary material and source code can be found at http://www.cs.duke.edu/∼amink/. …”
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    Domain-oriented edge-based alignment of protein interaction networks
  4. 1204
    “…Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html.…”
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    ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
  5. 1205
    “…It is available at: and the source code can be downloaded from: .…”
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    PhyloExplorer: a web server to validate, explore and query phylogenetic trees
  6. 1206
    “…Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. The source code is available, allowing for extending and reusing the software. …”
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    Pomelo II: finding differentially expressed genes
  7. 1207
    “…All software, including source code and documentation, is freely available. …”
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    designGG: an R-package and web tool for the optimal design of genetical genomics experiments
  8. 1208
    “…POIMs can be seen as a powerful generalization of sequence logos: they allow to capture and visualize sequence patterns that are relevant for the investigated biological phenomena. Availability: All source code, datasets, tables and figures are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/POIM. …”
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    POIMs: positional oligomer importance matrices—understanding support vector machine-based signal detectors
  9. 1209
    “…Many tools are multithreaded for parallelization in desktop or high-throughput computing environments, and most tasks can be performed in minutes for hundreds of datasets using a standard personal computer. Availability: Source code (C++) and documentation are available at http://function.princeton.edu/sleipnir and compiled binaries are available from the authors on request. …”
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    The Sleipnir library for computational functional genomics
  10. 1210
    “…Availability: The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/ Contact: sebi@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
  11. 1211
    por Li, Yunqi, Roy, Ambrish, Zhang, Yang
    Publicado 2009
    “…Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.…”
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    HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures
  12. 1212
    “…Our implementation, documentation, and source code for Core Hunter is available at…”
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    Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures
  13. 1213
    “…It is cross-platform compatible and the source code is freely available under the General Public License.…”
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    CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling
  14. 1214
    “…The search tool and the database are accessible via the World Wide Web at . Source code and binary distributions are available for academic use upon request.…”
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    MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
  15. 1215
    por Frank, Daniel N
    Publicado 2009
    “…CONCLUSION: Barcrawl and bartab can benefit researchers who are engaged in metagenomic projects that employ multiplexed specimen processing. The source code is released under the GNU general public license and can be accessed at .…”
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    BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
  16. 1216
    por Ali, Waqar, Deane, Charlotte M.
    Publicado 2009
    “…Availability: Program binaries and source code is freely available at http://www.stats.ox.ac.uk/research/bioinfo/resources Contact: ali@stats.ox.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.…”
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    Functionally guided alignment of protein interaction networks for module detection
  17. 1217
    “…Availability: The algorithms described here are implemented in C as part of the rip package. The source code of rip2 can be downloaded from http://www.combinatorics.cn/cbpc/rip.html and http://www.bioinf.uni-leipzig.de/Software/rip.html. …”
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    Target prediction and a statistical sampling algorithm for RNA–RNA interaction
  18. 1218
    “…Specialized views then allows ‘zooming in’ on the full annotation of interactions, interactors and their properties. 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 2010
  19. 1219
    “…Different export options allow easy usage of additional tools such as Cytoscape. Availability: Source code, pre-compiled binaries for different systems, a comprehensive tutorial, case studies and many additional datasets are freely available at http://www.ifr.ac.uk/dass/gui/. …”
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    DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data
  20. 1220
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    A methodology for projecting hospital bed need: a Michigan case study
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