Tag: Management

myProMS 3.9.3 – Management, Validation and Interpretation of MS-based Proteomic data

myProMS 3.9.3

:: DESCRIPTION

myProMS is a comprehensive bioinformatics environment (database and web server) for management of Mass Spectrometry (MS) protein identification data generated by database-search engines such as Mascot or Sequest. Multiple functionalities are available to mine, validate and interpret the data from both MS and biological point of views. In particular, biological interpretation of the results is facilitated through the use of sophisticated data comparison modules, annotation enrichments and links to external resources. myProMS was designed to optimize data access and sharing during collaboration between users with complementary expertises; typically MS experts and biologists.

::DEVELOPER

Institut Curie, Bioinformatics Core Facility

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  myProMS

:: MORE INFORMATION

Citation

Poullet P, Carpentier S, Barillot E.
myProMS, a web server for management and validation of mass spectrometry-based proteomic data.
Proteomics. 2007, 7 (15):2553-6.

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

Proteios

:: 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.

PhenoMan 1.0RC – Exploration and Management of Phenotype data

PhenoMan 1.0RC

:: DESCRIPTION

Phenoman is freeware that provides approaches for efficient exploration and management of phenotype data.

::DEVELOPER

PhenoMan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python
  • R package

:: DOWNLOAD

 PhenoMan

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 1;30(3):442-4. doi: 10.1093/bioinformatics/btt682. Epub 2013 Dec 12.
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants.
Li B1, Wang G, Leal SM.

mtDNAmanager – Management and Quality Analysis of Mitochondrial DNA Control Region Sequences

mtDNAmanager

:: DESCRIPTION

mtDNAmanager provides a convenient web interface to analyze, query and store human mtDNA control region sequences

::DEVELOPER

Yonsei DNA Profiling Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 17;9:483. doi: 10.1186/1471-2105-9-483.
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences.
Lee HY1, Song I, Ha E, Cho SB, Yang WI, Shin KJ.

PMx 1.6.2 / PMxLite – Software for Pedigree Analysis and Management

PMx 1.6.2 / PMxLite

:: DESCRIPTION

PMx is a package of demographic and genetic analysis tools to assist with the management of breeding programs for wildlife species.

PMxLite: PMx Made Simpler

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PMx

:: MORE INFORMATION

Citation

Lacy, R.C., J.D. Ballou, & J.P. Pollak. 2012.
PMx: Software package for demographic and genetic analysis and management of pedigreed populations.
Methods in Ecology & Evolution 3:433-437.

GEMAT 2.0 – Genomics Experiment Management and Analysis Tool

GEMAT 2.0

:: DESCRIPTION

GEMAT is an information management system designed as client-server tool for handling variety of microarray platform eg., Affymetrix GeneChip information. It has builtin analytical tools for performing data mining and posting microarry data to endusers.

::DEVELOPER

Bioinformatics Group, Roskamp Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • LAMPP (Linux-Apache-MySQL-Perl/PHP) environment

:: DOWNLOAD

 GEMAT

:: MORE INFORMATION

Citation

Venkatarajan Mathura, Deepak Kolippakkam, Fiona Crawford, Michael Mullan., 2005
“GEMAT: Genomic Experiment Management and Analysis Tool”,
ISMB 2005

SLIMarray 0.3.5 – Lightweight software for Microarray Facility Management

SLIMarray 0.3.5

:: DESCRIPTION

SLIMarray is a Ruby on Rails database-backed web application that allows microarray facilities to track inventories of arrays, hybridizations performed and charge accrued for services by their customers. Beyond just tracking these separate pieces of information, it provides added value by utilizing the relationships between them. For instance, when hybridizations are entered, transactions are automatically created to deduct used microarrays from the proper inventories and appropriate charges are recorded.

::DEVELOPER

the Institute for Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Windows
  • Web Server
  • SQL
  • RUBY

:: DOWNLOAD

  SLIMarray

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2006 Oct 26;1:5.
SLIMarray: lightweight software for microarray facility management.
Marzolf B, Troisch P.

SNPHunter 1.75 – dbSNP Search & Management

SNPHunter 1.75

:: DESCRIPTION

SNPHunter is a tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering.

::DEVELOPER

Program for Population Genetics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SNPHunter

:: MORE INFORMATION

Citation

Lin Wang, Simin Liu, Tianhua Niu, Xin Xu (2005).
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
BMC bioinformatics. 6: 60.

SeqServe 0.1 – Management of Sequencing Samples

SeqServe 0.1

:: DESCRIPTION

SeqServe is a package for small to medium scale sequencing facilites to manage users, groups, bookings, distribution and post-processing of sequencing samples.SeqServe is currently primarily aimed at ABI sequencers.

::DEVELOPER

the Bioinformatics and Computational Biology Unit at the University of Pretoria

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL
  • PHRED
  • BCM Trace Viewer

:: DOWNLOAD

 SeqServe

:: MORE INFORMATION

TAMEE 1.1 – Tissue Array Management and Evaluation Environment

TAMEE 1.1

:: DESCRIPTION

TAMEE is a web-based database application for the management and analysis of data resulting from the production and experimental use of TMAs. In addition to production and experimental parameters images generated during the different stages of the TMA workflow are stored. Parameter values are based on structured classifications to ensure consistent database content which is the basis to yield biologically meaningful results in subsequent data analysis. Therefore existing public classifications are used and new controlled vocabularies have been defined in the context of the application. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be automatically evaluated with a set of predefined analysis algorithms. Additional algorithms for the evaluation of tissue cores can be added to the application via a plug-in interface. Downstream analysis of the results is facilitated via a set of standard queries. More complex queries can be formulated with the help of a flexible query generator.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  •  MySQL

:: DOWNLOAD

 TAMEE

:: MORE INFORMATION

Citation

Thallinger GG, Baumgartner K, Pirklbauer M, Uray M, Pauritsch E, Mehes G, Buck CR, Zatloukal K, Trajanoski Z.
TAMEE: data management and analysis for tissue microarrays.
BMC Bioinformatics. 2007. 8:81.

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