Tag: Analysis system

SGAtools 20131030 – Web-based Analysis System for Designer Genetic Screens

SGAtools 20131030

:: DESCRIPTION

SGAtools offers a single stop solution for analysing data from genetic screens. There are three steps to the analysis pipeline, each of which can also be run separately from the rest. First, images of plates with colonies are processed to give quantified colony sizes for the screen. Next, the colony sizes are normalised and filtered within plates, taking into account position effects and other confounding factors.

::DEVELOPER

Boone lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 SGAtools

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul 1;41(Web Server issue):W591-6. doi: 10.1093/nar/gkt400. Epub 2013 May 15.
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.
Wagih O, Usaj M, Baryshnikova A, Vandersluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.

XMAS – eXperiential Microarray Analysis System

XMAS

:: DESCRIPTION

XMAS is an open-source, platform-independent web application for a new type of interactive, “sit-forward” microarray analysis.

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

XMAS

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 14:S10. doi: 10.1186/1471-2105-14-S14-S10. Epub 2013 Oct 9.
Towards human-computer synergetic analysis of large-scale biological data.
Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gormley M, Stillman J, Fisher S.

QSpec 1.0 / QSpec-Simu 1.0 – A Raman Spectrum Acquisition and Analysis System for Single-Cell

QSpec 1.0 / QSpec-Simu 1.0

:: DESCRIPTION

QSpec is an open-source framework of microorganism single-cell experimental platform that could support the full cycle of single-cell phenotyping: instrument control (including RACS platform control and microfluidic device control), single-cell image analysis, single-cell Raman profiling, single-cell profile comparison, etc.

QSpec-Simu is an open-source framework of virtual microorganism single-cell experimental platform

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

QSpec / QSpec-Simu

:: MORE INFORMATION

Citation

Lihui R.; Xiaoquan S.; Yun W.; Jian X.; Kang N.,
QSpec: online control and data analysis system for single-cell Raman spectroscopy.
PeerJ. 2014 Jun 26;2:e436. doi: 10.7717/peerj.436. eCollection 2014.

EDGE-pro 1.3.1 – Prokaryotic Transcriptome Analysis system

EDGE-pro 1.3.1

:: DESCRIPTION

EDGE-pro, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EDGE-pro

:: MORE INFORMATION

Citation:

T. Magoc, D. Wood, and S.L. Salzberg.
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
Evolutionary Bioinformatics vol.9, pp.127-136, 2013.

DEODAS 0.2.0 -DEgenerate Oligo Nucleotide Design & Analysis System

DEODAS 0.2.0

:: DESCRIPTION

DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.

::DEVELOPER

Karl Diedrich

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • gtkmm, available at http://gtkmm.sourceforge.net/
  • libsigc++, available at http://libsigc.sourceforge.net/
  • python
  • pygtk
  • pygnome
  • postgresql

:: DOWNLOAD

 DEODAS

:: MORE INFORMATION

Citation

Karl Diedrich
DEODAS: A DEgenerate Oligonucleotide Design and Analysis System 

Image 3.10 – The Fingerprint Image Analysis system

Image 3.10

:: DESCRIPTION

Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments.Image extracts a normalized band pattern for each lane (clone) on a gel. To achieve this several procedures are run on each gel in turn. The cycle starts when the user scans the film image or otherwise imports gel image data. The cycle ends when the normalized band position are transferred to a database and FPC takes over and matches up the clones to assemble contigs.

::DEVELOPER

Image Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Image

:: MORE INFORMATION