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Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT: QuinlanLab, University of Utah: Bioclipse: Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows [1] Eclipse Public: The Bioclipse ...
This server includes many bioinformatics tools that are widely useful in many areas of genomics research. Users can create logins, and save histories, workflows, and datasets on the server. These saved items can also be shared with others. As open-source software that can be downloaded, installed and customized to address specific needs. [20]
Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. ContextMap was developed to overcome some limitations of other mapping approaches, such as resolution of ambiguities. The central idea of this tool is to consider reads in gene expression context, improving this way alignment accuracy.
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GMOD: GMOD (Generic Model Organism Database) is a collection of open-source tools for building and sharing genome databases. It provides a framework for integrating genomic data with other biological data types, such as proteomics and metabolomics, and allows for the sharing of data and analysis with collaborators.
Open source software provides a platform for computational biology where everyone can access and benefit from software developed in research. PLOS cites [citation needed] four main reasons for the use of open source software: Reproducibility: This allows for researchers to use the exact methods used to calculate the relations between biological ...
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and ...
NGS platforms Platform Template preparation Chemistry Max read length (bases) Run times (days) Max Gb per Run Roche 454 Clonal-emPCR Pyrosequencing 400‡ 0.42 0.40-0.60 GS FLX Titanium Clonal-emPCR Pyrosequencing 400‡ 0.42 0.035 Illumina MiSeq Clonal Bridge Amplification Reversible Dye Terminator 2x300 0.17-2.7 15 Illumina HiSeq