Tag: Manager

Refgenie v0.12.1 / refgenieserver v0.7.0 – Reference Genome Resource Manager

Refgenie v0.12.1 / refgenieserver v0.7.0

:: DESCRIPTION

Refgenie manages storage, access, and transfer of reference genome resources.

Refgenieserver is containerized code that hosts genome assets that can be automatically downloaded by the refgenie command-line interface.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Refgenie / Refgenieserver

:: MORE INFORMATION

Citation

Stolarczyk M, Reuter VP, Smith JP, Magee NE, Sheffield NC.
Refgenie: a reference genome resource manager.
Gigascience. 2020 Feb 1;9(2):giz149. doi: 10.1093/gigascience/giz149. PMID: 31995185; PMCID: PMC6988606.

SAM 1.0 – Sequence Assembly Manager

SAM 1.0

:: DESCRIPTION

SAM (Sequence Assembly Manager)is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

 

:: SCREENSHOTS

: REQUIREMENTS

:: DOWNLOAD

  SAM

:: MORE INFORMATION

Citation

Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. (2005)
Management and Visualization of Whole Genome Shotgun Assemblies using SAM.
Biotechniques. 38:715-720

BRM 2.3 – Bioinformatics Resource Manager

BRM 2.3

:: DESCRIPTION

BRM (Bioinformatics Resource Manager) is a software program that provides robust middleware architecture to link scientific applications and heterogeneous data sources. Bioinformaticists are using this framework to automate multidisciplinary data mining processes used for high-throughput molecular profiling. The software created by our research team will allow communication between different software tools from within BRM.

::DEVELOPER

Pacific Northwest National Laboratory (PNNL)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BRM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Nov 23;13:311. doi: 10.1186/1471-2105-13-311.
Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools.
Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, Waters KM.

Shah AR, M Singhal, KR Klicker, EG Stephan, HS Wiley, KM Waters. 2007.
“Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager.”
Bioinformatics 2007 23(7):906-909; doi:10.1093/bioinformatics/btm031.

Database Manager 2.1 – FASTA Database Manager

Database Manager 2.1

:: DESCRIPTION

Database Manager stores all your sequence databases in a single folder (repository). It offers :

  • conservation of metadata : database origin, species, number of protein, download site, …
  • translation of DNA into protein
  • creation of decoy protein databases (protein reverse, random, peptide reverse
  • combination of different existing databases

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

Fastamanager

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 Database Manager

:: MORE INFORMATION

Biota 3.00 – Biodiversity Database Manager

Biota 3.00

:: DESCRIPTION

Biota manages specimen-based, spatially and taxonomically referenced data for ecologists, conservation biologists, evolutionary biologists, systematists, museums and herbaria.

::DEVELOPER

Robert K. Colwell

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 Biota

:: MORE INFORMATION

Citation

Colwell, R. K. 2004.
Biota 2: The biodiversity database manager.
Sinauer Associates, Sunderland, MA.

Handlebar 2.2.2 – Web Based Sample Inventory Manager

Handlebar 2.2.2

:: DESCRIPTION

Handlebar is a web based sample inventory manager, originally designed to meet the needs of researchers in the NERC PG&P research projects, it is now available for wider use. It is simple to use, allows a central database to serve users over multiple sites and permits the administrator to easily define new item templates for different types of sample. Linking between related samples is supported. The system is designed to work with printed barcode labels and functions are provided to print labels with Zebra brand barcode printers using the EPL protocol.

::DEVELOPER

the NEBC and the University of Manchester

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Handlebar

:: MORE INFORMATION

If you are interested in using the software or have any questions please contact the author via helpdesk@nebc.nox.ac.uk