Tag: Experiment

CI Micro v2.1 – Analyzing Time-lapse Experiments of Cell Migration, Invasion and Wound Healing assays

CI Micro v2.1

:: DESCRIPTION

CI Micro was developed primary for quickly analyzing time-lapse experiments of cell migration, invasion and wound healing assays. Time-lapse experiments saved in Leica’s LIF or (auto-saved) XLEF files can be opened with no delay in loading time. Interactive measurements can be done by the area or counting tool and are save together with experimental data. Extra options are Movie Export, 3D features and support for TIFF files.

::DEVELOPER

the Cellular Imaging Core Facility

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  •  .NET Framework 4.6.1 or higher

:: DOWNLOAD

CI Micro

:: MORE INFORMATION

TEXMEX 0.3 – Treatment Effect eXplorer for Microbial Ecology eXperiments

TEXMEX 0.3

:: DESCRIPTION

Texmex is designed to normalize OTU count data and correct for community composition changes that are common to a control and experimental unit.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • R

:: DOWNLOAD

TEXMEX

:: MORE INFORMATION

Citation

Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, Hazen TC, Alm EJ.
A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.
PLoS One. 2016 May 6;11(5):e0154804. doi: 10.1371/journal.pone.0154804. PMID: 27152415; PMCID: PMC4859510.

GLAMM 2.2.4 – Interactive Viewer for Metabolic Pathways and Experiments

GLAMM 2.2.4

:: DESCRIPTION

GLAMM (The Genome-Linked Application for Metabolic Maps) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. We use Microbes Online as the first of what will ultimately be multiple sources for metabolic reconstruction and pathway data, including custom, user-uploadable networks.

::DEVELOPER

The Arkin laboratory 

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

John T. Bates; Dylan Chivian; Adam P. Arkin
GLAMM: Genome-Linked Application for Metabolic Maps
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr433

Virtual Cat 3.0.0 – Simulation of an Anaesthetised Cat Experiment

Virtual Cat 3.0.0

:: DESCRIPTION

The Virtual Cat is a simulation of an anaesthetised cat experiment – a whole animal preparation which is used as a tool for screening the actions of pharmaceutical compounds on the cardiovascular and skeletal muscle systems. The simulation displays the effects of drugs on the cat’s blood pressure, heart rate, skeletal muscle and nictitating membrane contractions.

::DEVELOPER

the Strathclyde Institute of Pharmacy and Biomedical Sciences

:: SCREENSHOTS

VirtualCat

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 Virtual Cat

:: MORE INFORMATION

Molgenis 9.1.0 – Generate Databases for Life Science Experiments

Molgenis 9.1.0

:: 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

Molgenis team

:: 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.

sapFinder 1.26.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.26.0

:: 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.

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)

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.

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

CSIRO Transformational Bioinformatics

:: 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.