xGDBvm – A Cloud-enabled Genome Annotation Platform

xGDBvm

:: DESCRIPTION

xGDBvm is a web-based platform for annotating and visualizing eukaryotic genomes.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux
  • PHP

:: DOWNLOAD

xGDBvm

:: 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.

PIVOT v1.0.1 – Platform for Interactive analysis and Visualization Of Transcriptomics data

PIVOT v1.0.1

:: 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

the Kim Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

PIVOT

:: 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.

Proteios 2.19.0 – Multi-user Platform for Analysis and Management of Proteomics data

Proteios 2.19.0

:: 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

  Proteios

:: 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.

GEDpm-cg – Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

GEDpm-cg

:: 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

  • Web server
  • Python

:: DOWNLOAD

GEDpm-cg

:: 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.

WASP v1.0 – Web-Accessible Single Cell RNA-Seq Processing Platform

WASP v1.0

:: 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

  • Linux / WIndows / MacOS
  • R
  • Python

:: DOWNLOAD

WASP

:: 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.

inGAP 3.1.1 – Integrated Next-gen Genome Analysis Platform

inGAP 3.1.1

:: 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

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 inGAP

:: 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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VESPA 1.1.1 – Visual Analytics Platform for Exploring Proteogenomics data

VESPA 1.1.1

:: 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

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 VESPA

:: 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.

Bisque 0.5.8 – Platform for Bioimage Analysis & Management

Bisque 0.5.8

:: 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

Bisque

:: 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.

Lynx v3.0 – Integrated Systems Biology Platform

Lynx v3.0

:: DESCRIPTION

Lynx is a database and knowledge extraction engine for integrative medicine

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: 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.

GenomeVIP v1.2.1 – Cloud based Genome Variant Investigation Platform

GenomeVIP v1.2.1

:: 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

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GenomeVIP

:: 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.

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