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  1. 1501
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    DADOS-Prospective: an open source application for Web-based prospective data collection
  2. 1502
    “…A user-friendly web interface, Java source code and executables are available at .…”
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    A novel ensemble learning method for de novo computational identification of DNA binding sites
  3. 1503
    por Ross, Robert M, Corry, David B
    Publicado 2007
    “…The actual program and the open source code are also available free over the Internet at . …”
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    Software for interpreting cardiopulmonary exercise tests
  4. 1504
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    Bioinformatics process management: information flow via a computational journal
  5. 1505
    por Parker, Nicolas J, Parker, Andrew G
    Publicado 2008
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    Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data
  6. 1506
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    OSPACS: Ultrasound image management system
  7. 1507
    por Demeure, Olivier, Lecerf, Frédéric
    Publicado 2008
    “…CONCLUSION: Written in PERL, it assures a maximum portability to other operating systems (OS) and the source code availability for user modifications. Except for the simulation mode which could be time consuming, MarkerSet can compute results in a very short time.…”
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    MarkerSet: a marker selection tool based on markers location and informativity in experimental designs
  8. 1508
    “…The algorithm and features are discussed and demonstrated on actual design runs. Source code is available on request.…”
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    Model-based probe set optimization for high-performance microarrays
  9. 1509
    “…A convenient web service allows users to directly convert SBML to various formats, including DVI, L(a)T(E)X and PDF, and provides many settings for customization. Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX. …”
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    SBML2L(a)T(E)X: Conversion of SBML files into human-readable reports
  10. 1510
    “…This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.…”
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    Implementation of GenePattern within the Stanford Microarray Database
  11. 1511
    “…Availability: A data table with the training sequences is available as supplementary material. Source code is available online at http://www.inference.phy.cam.ac.uk/os252/projects/quadruplexes Contact: os252@cam.ac.uk; jlh29@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    Predicting and understanding the stability of G-quadruplexes
  12. 1512
    “…Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.…”
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    Stochastic sampling of the RNA structural alignment space
  13. 1513
    “…However, RAF requires nearly an order of magnitude less time than other simultaneous folding and alignment methods, thus making it especially appropriate for high-throughput studies. Availability: Source code for RAF is available at:http://contra.stanford.edu/contrafold/ Contact: chuongdo@cs.stanford.edu…”
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    A max-margin model for efficient simultaneous alignment and folding of RNA sequences
  14. 1514
    por Lee, Thomas J., Paulsen, Ian, Karp, Peter
    Publicado 2008
    “…Pathway Tools is freely available to researchers at non-commercial institutions, including source code; a fee applies to commercial institutions. …”
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    Annotation-based inference of transporter function
  15. 1515
    “…The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.…”
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    Rapid prototyping of 3D DNA-origami shapes with caDNAno
  16. 1516
    por Leung, Garmay, Eisen, Michael B.
    Publicado 2009
    “…We also show that regulatory sequences can be distinguished from surrounding sequences by local sequence dissimilarity, a novel feature in identifying regulatory sequences across a genome. Source code for WPH-finder is available for download at http://rana.lbl.gov/downloads/wph.tar.gz.…”
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    Identifying Cis-Regulatory Sequences by Word Profile Similarity
  17. 1517
    “…CONCLUSION: Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at .…”
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    Genoviz Software Development Kit: Java tool kit for building genomics visualization applications
  18. 1518
    “…Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. …”
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    Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars
  19. 1519
    “…MetaTM is made available both as downloadable source code and as DAS server at…”
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    MetaTM - a consensus method for transmembrane protein topology prediction
  20. 1520
    “…Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).…”
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    Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
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