Flux Simulator 1.2.1 – Modeling RNA-Seq Experiments

Flux Simulator 1.2.1

:: DESCRIPTION

The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Flux Simulator

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

Scotty – Power Analysis for RNA Seq Experiments

Scotty

:: DESCRIPTION

Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • MatLab

:: DOWNLOAD

 Scotty

:: MORE INFORMATION

Citation

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.
Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT.
Bioinformatics. 2013 Mar 1;29(5):656-7. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.

Virtual NMJ 2.1.9 – Simulation of an Experiment Recording the Electrical Potentials

Virtual NMJ 2.1.9

:: DESCRIPTION

The Virtual NMJ is a simulation of an experiment recording the electrical potentials associated with neuromuscular transmission at the skeletal neuromuscular junction. The simulation allows you to observe the muscle action potential (AP) and endplate potentials (EPPs) evoked by either nerve stimulation or by direct current stimulation of the muscle fibre. The effects of a variety of drugs and of changes to ionic composition of the extracellular solution on the AP and EPPs can be studied.

::DEVELOPER

the Strathclyde Institute of Pharmacy and Biomedical Sciences

:: SCREENSHOTS

VirtualNMJ

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  Virtual NMJ

:: MORE INFORMATION

NGSANE 0.5.2.0 – Analysis Framework for Biological Data from High Throughput Experiments

NGSANE 0.5.2.0

:: DESCRIPTION

NGSANE (Next Generation Sequencing ANalysis for Enterprises ) is a framework for advanced production informatics of Next Generation Sequencing libraries.

::DEVELOPER

BauerLab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NGSANE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1471-2. doi: 10.1093/bioinformatics/btu036. Epub 2014 Jan 26.
NGSANE: a lightweight production informatics framework for high-throughput data analysis.
Buske FA1, French HJ, Smith MA, Clark SJ, Bauer DC.

BEW 2.1.0 – Biofilms Experiment Workbench

BEW 2.1.0

:: DESCRIPTION

BEW is a novel software workbench for the operation and analysis of Biofilms experimental data.

::DEVELOPER

SING Group.

:: SCREENSHOTS

bew

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • R

:: DOWNLOAD

 BEW

:: MORE INFORMATION

Citation

Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.
Pérez-Rodríguez G, Glez-Peña D, Azevedo NF, Pereira MO, Fdez-Riverola F, Lourenço A.
Comput Methods Programs Biomed. 2015 Mar;118(3):309-21. doi: 10.1016/j.cmpb.2014.12.005.

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

sapFinder 1.7.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.7.0

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

 Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R
  • BioCOnductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Jul 22. pii: btu397.

Findings 1.2.2 – Your Lab Notebook

Findings 1.2.2

:: DESCRIPTION

Findings is a new app for mac designed for scientists who wish to leave the paper lab notebook behind and step into the digital world.

::DEVELOPER

Findings team

:: SCREENSHOTS

Findings

:: REQUIREMENTS

  •  Mac OsX

:: DOWNLOAD

Findings

:: MORE INFORMATION

ICeE 2.10 – Interface for C. Elegans Experiments

ICeE 2.10

:: DESCRIPTION

ICeE is a database with a Web-browser interface that allows you to enter experiments for the nematode C. elegans and to search efficiently in this database.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

ICeE

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Apache httpd
  • MySQL
  • PHP

:: DOWNLOAD

 ICeE

:: MORE INFORMATION

Molgenis 15.04 – Generate Databases for Life Science Experiments

Molgenis 15.04

:: DESCRIPTION

MOLGENIS ( MOLecular GENetics Information Systems) is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services. The MOLGENIS platform allows you to automatically generate rich database software to your specifications, including web user interfaces to manage and query your data, various database back ends to store your data, and programmatic interfaces to the R language and web services. You tell MOLGENIS what to generate using an data model and user interface model described in XML; at the push of a button MOLGENIS translates this model into SQL, Java and R program files. Also documentation is generated. While the standard generated MOLGENIS is sufficient for most data management needs, MOLGENIS also allows you to plug in handwritten software components that build on the auto-generated software platform.

::DEVELOPER

the Genomics Coordination Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Molgenis 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12.
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.