:: DESCRIPTION
Cluster Flow is a pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
::DEVELOPER
Phil Ewels @ the Science for Life Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ewels P, Krueger F, Käller M, Andrews S.
Cluster Flow: A user-friendly bioinformatics workflow tool.
F1000Res. 2016 Dec 6;5:2824. doi: 10.12688/f1000research.10335.2. PMID: 28299179; PMCID: PMC5310375.
:: DESCRIPTION
BMT is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Iqbal MN, Rasheed MA, Awais M, Chammam W, Kanwal S, Khan SU, Saddick S, Tlili I.
BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis.
Genomics. 2020 Nov;112(6):4561-4566. doi: 10.1016/j.ygeno.2020.08.010. Epub 2020 Aug 10. PMID: 32791200.
:: DESCRIPTION
BioCRF is an implementation of Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) , an extension of linear HCRF to include prior knowledge about the problem at hand by means of a regular grammar. This results very useful in several Bioinformatics problems where only solution that agree with a regular grammar rules are biologically meaningful.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Piero Fariselli, Castrense Savojardo, Pier L Martelli and Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Algorithms for Molecular Biology 2009, 4:13
:: DESCRIPTION
GC4S is an open-source library that provides a bioinformatics-oriented collection of GUI Components for (Java) Swing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
López-Fernández H, Reboiro-Jato M, Glez-Peña D, Laza R, Pavón R, Fdez-Riverola F.
GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.
PLoS One. 2018 Sep 20;13(9):e0204474. doi: 10.1371/journal.pone.0204474. PMID: 30235322; PMCID: PMC6147514.
:: DESCRIPTION
Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …).
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014;15 Suppl 1:S3. doi: 10.1186/1471-2105-15-S1-S3. Epub 2014 Jan 10.
Explorative search of distributed bio-data to answer complex biomedical questions.
Masseroli M, Picozzi M, Ghisalberti G, Ceri S.
:: DESCRIPTION
BioHEL is an evolutionary learning system designed to handle with large-scale bioinformatic datasets.
BioHEL RPE is a standalone program which takes a set of rules generated with BioHEL and applies a series of memetic operators over the individual rules and the whole rule set to increase their generality and reduce their complexity.
::DEVELOPER
Interdisciplinary Computing and Complex BioSystems (ICOS) research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M.A. Franco, N. Krasnogor, J. Bacardit
Speeding up the evaluation of evolutionary learning systems using GPGPUs
in Proceedings of the 12th annual conference on Genetic and evolutionary computation – GECCO ’10, p.1039, Portland, Oregon, USA, 2010
J. Bacardit, E.K. Burke, N. Krasnogor
Improving the scalability of rule-based evolutionary learning
in Memetic Computing, 1(1):55-67, March 2009
M.A. Franco, N. Krasnogor, J. Bacardit
Post-processing operators for decision lists
in Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference – GECCO ’12, p.847, Philadelphia, Pennsylvania, USA, 2012
:: DESCRIPTION
The Taiji software is an integrative multi-omics data analysis framework. It can be used as a standalone pipeline to analyze ATAC-seq, RNA-seq, single cell ATAC-seq or Drop-seq data. However, the uniqueness and the power of Taiji really lie in its ability to integrate diverse datasets and use these information in a clever way to construct regulatory network and identify candidate driver genes.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang K, Wang M, Zhao Y, Wang W.
Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development.
Sci Adv. 2019 Mar 27;5(3):eaav3262. doi: 10.1126/sciadv.aav3262. PMID: 30944857; PMCID: PMC6436936.
:: DESCRIPTION
birgHPC (Bioinformatic Research Group High Performance Computing) is a free Linux Live CD distribution based on PelicanHPC and Debian Live.birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir.
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.
Bioinformatics. Volume 27, Issue 9. pp 1320-1321.
:: DESCRIPTION
The BTL provides generic mathematical components that allow C++ programmers to more rapidly construct applications that model biological entities.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The DART (DNA, Amino and RNA Tests.)library includes a number of bioinformatics programs, including: stemloc for RNA alignment; xrate for phylo-grammars; phylocomposer and other statistical alignment programs in the Handel package; and more.The programs use statistical algorithms (MCMC, EM) to impute multiple alignments, annotations and other unseen evolutionary parameters from sequence data. All are based on stochastic grammars or state-machine models of sequence mutation and natural selection.
::DEVELOPER
Ian Holmes, Berkeley
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
