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  1. 3341
    “…By providing availability of the software and its source code we hope to facilitate future related research.…”
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    GEDAE-LaB: A Free Software to Calculate the Energy System Contributions during Exercise
  2. 3342
    “…In comparison with other SNP detection approaches, 4Pipe4 showed the best validation ratio, retrieving a smaller number of SNPs but with a considerably lower false positive rate than other methods. 4Pipe4’s source code is available at https://github.com/StuntsPT/4Pipe4.…”
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    4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information
  3. 3343
    por Daily, Jeff
    Publicado 2016
    “…The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. …”
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    Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
  4. 3344
    “…Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. …”
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    Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data
  5. 3345
    “…We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). …”
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    Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts
  6. 3346
    “…We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page: https://github.com/zubekj/broad_peaks. …”
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    Computational inference of H3K4me3 and H3K27ac domain length
  7. 3347
    “…The software is open source (GPLv3 license), and operates on the major platforms (Windows, Mac, and Linux). The complete source code can be downloaded from http://infectio.github.io/index.html. …”
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    Infectio: a Generic Framework for Computational Simulation of Virus Transmission between Cells
  8. 3348
    “…Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available. …”
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    SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
  9. 3349
    “…Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID. …”
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    Identifying micro-inversions using high-throughput sequencing reads
  10. 3350
    “…Availability and implementation: The source code of BNMF and tutorials on how to use the software to extract local clusters from contact maps are available at http://yiplab.cse.cuhk.edu.hk/bnmf/. …”
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    A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps
  11. 3351
    “…Availability and Implementation: The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. …”
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    SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing
  12. 3352
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    SV-STAT accurately detects structural variation via alignment to reference-based assemblies
  13. 3353
    “…Our bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/, and the source code is provided at the methods page. CONCLUSION: An online bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/. …”
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    bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming
  14. 3354
    por Clark, Lindsay V., Sacks, Erik J.
    Publicado 2016
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    TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data
  15. 3355
    “…It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan. …”
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    MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information
  16. 3356
    “…Availability and Implementation: Source code, executable versions, manuals and example data of UniCon3D for Linux and OSX are freely available to non-commercial users at http://sysbio.rnet.missouri.edu/UniCon3D/. …”
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    UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
  17. 3357
    “…CONCLUSION: DeepQA is a useful deep learning tool for protein single model quality assessment and protein structure prediction. The source code, executable, document and training/test datasets of DeepQA for Linux is freely available to non-commercial users at http://cactus.rnet.missouri.edu/DeepQA/. …”
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    DeepQA: improving the estimation of single protein model quality with deep belief networks
  18. 3358
    por Aken, Bronwen L., Achuthan, Premanand, Akanni, Wasiu, Amode, M. Ridwan, Bernsdorff, Friederike, Bhai, Jyothish, Billis, Konstantinos, Carvalho-Silva, Denise, Cummins, Carla, Clapham, Peter, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah E., Janacek, Sophie H., Juettemann, Thomas, Keenan, Stephen, Laird, Matthew R., Lavidas, Ilias, Maurel, Thomas, McLaren, William, Moore, Benjamin, Murphy, Daniel N., Nag, Rishi, Newman, Victoria, Nuhn, Michael, Ong, Chuang Kee, Parker, Anne, Patricio, Mateus, Riat, Harpreet Singh, Sheppard, Daniel, Sparrow, Helen, Taylor, Kieron, Thormann, Anja, Vullo, Alessandro, Walts, Brandon, Wilder, Steven P., Zadissa, Amonida, Kostadima, Myrto, Martin, Fergal J., Muffato, Matthieu, Perry, Emily, Ruffier, Magali, Staines, Daniel M., Trevanion, Stephen J., Cunningham, Fiona, Yates, Andrew, Zerbino, Daniel R., Flicek, Paul
    Publicado 2017
    “…All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.…”
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    Ensembl 2017
  19. 3359
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    LitDB - Keeping Track of Research Papers From Your Institute Made Simple
  20. 3360
    “…In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. …”
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    WebGIVI: a web-based gene enrichment analysis and visualization tool
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