:: DESCRIPTION
xGDBvm is a web-based platform for annotating and visualizing eukaryotic genomes.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Duvick J, Standage DS, Merchant N, Brendel VP.
xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.
Plant Cell. 2016 Apr;28(4):840-54. doi: 10.1105/tpc.15.00933. Epub 2016 Mar 28. PMID: 27020957; PMCID: PMC4863385.
:: DESCRIPTION
PIVOT is an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J.
PIVOT: platform for interactive analysis and visualization of transcriptomics data.
BMC Bioinformatics. 2018 Jan 5;19(1):6. doi: 10.1186/s12859-017-1994-0. PMID: 29304726; PMCID: PMC5756333.
:: DESCRIPTION
Proteios SE (or ProSE) is meant to be installed on a local server in a proteomics laboratory.
::DEVELOPER
Jari Häkkinen @ Lund University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Proteome Res. 2009 Jun;8(6):3037-43. doi: 10.1021/pr900189c.
The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data.
Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F.
:: DESCRIPTION
GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results.
::DEVELOPER
Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H.
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum.
Front Bioeng Biotechnol. 2021 Oct 15;9:768289. doi: 10.3389/fbioe.2021.768289. PMID: 34722482; PMCID: PMC8554027.
:: DESCRIPTION
WASP is a software covering the full range of analysis steps of a typical single-cell RNA sequencing workflow for Drop-Seq-based scRNA-Seq data.
::DEVELOPER
Bioinformatics and Systems Biology, Justus-Liebig-University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A.
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
BMC Genomics. 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6. PMID: 33736596; PMCID: PMC7977290.
:: DESCRIPTION
inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.It does not have any read length restriction. It can handle 454 sequencing and/or Illumina Solexa sequencing and/or Sanger sequencing data sets.
::DEVELOPER
Ji Qi (qij@fudan.edu.cn) and Fangqing Zhao (zhfq@mail.biols.ac.cn)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2010 Jan 1;26(1):127-9. Epub 2009 Oct 30.
inGAP: an integrated next-generation genome analysis pipeline.
Qi J, Zhao F, Buboltz A, Schuster SC.
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:: DESCRIPTION
VESPA (Visual Exploration and Statistics to Promote Annotation) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.
::DEVELOPER
Computational Biology & Bioinformatics, Pacific Northwest National Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.
BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.
:: DESCRIPTION
Bisque (Bio-Image Semantic Query User Environment) was developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.
::DEVELOPER
The Center for Bio-Image Informatics
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kristian Kvilekval, Dmitry Fedorov, Boguslaw Obara, Ambuj Singh and B.S. Manjunath,
“Bisque: A Platform for Bioimage Analysis and Management”
Bioinformatics, vol. 26, no. 4, pp. 544-552, Feb. 2010.
:: DESCRIPTION
Lynx is a database and knowledge extraction engine for integrative medicine
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Sulakhe D, Xie B, Taylor A, D’Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N.
Lynx: a knowledge base and an analytical workbench for integrative medicine.
Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20. PMID: 26590263; PMCID: PMC4702889.
:: DESCRIPTION
GenomeVIP is a web application platform for performing variant discovery on Amazon’s Web Service (AWS) cloud or on local high-performance computing clusters.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny? D, Raphael BJ, Wendl MC, Ding L.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation.
Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612; PMCID: PMC5538560.
