Tag: Information

BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4 – Information about Mouse and Human CD Molecules

BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4

:: DESCRIPTION

BioLegend CD Posters / BioLegend Tools for iPad provides you with important information about your mouse and human CD Molecules, Cytokines and Chemokines.

BioLegend Tools for iPad also includes BioLegend pathway posters, an antibody usage calculator, and a lab timer. What’s more it is optimized for the iPad for speed and clarity.

::DEVELOPER

BioLegend

:: SCREENSHOTS

bcp

:: REQUIREMENTS

  • iPhone /  iPad

:: DOWNLOAD

 BioLegend CD Posters / BioLegend Tools for iPad

:: MORE INFORMATION

WIST 1.1 – The Workflow Information Storage Toolkit

WIST 1.1

:: DESCRIPTION

WIST is a template-based toolkit to facilitate rapid LIMS (Laboratory Information Management System) development. WIST is designed to create LIMS modules with a web-based front end and a SQL database back end, along with a repository for larger data objects (e.g., files) that are impractical to store in SQL tables.

::DEVELOPER

The VIMSS (Virtual Institute of Microbial Stress and Survival)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Apach
  • MySQL
  • Perl

:: DOWNLOAD

 WIST

:: MORE INFORMATION

Citation

WIST: toolkit for rapid, customized LIMS development.
Huang YW, Arkin AP, Chandonia JM.
Bioinformatics. 2011 Feb 1;27(3):437-8. doi: 10.1093/bioinformatics/btq676. Epub 2011 Jan 21.

EcologIE PMCMiner 0.1 – Extract Information about Species Interactions from the Ecological Literature

EcologIE PMCMiner 0.1

:: DESCRIPTION

 EcologIE PMCMiner is a set of tools for extracting putative multispecies interaction data from articles in the Pubmed Open Access Subset.

::DEVELOPER

Bergman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 EcologIE PMCMiner

:: MORE INFORMATION

Citation:

An exploration of mining species interaction data from the ecology literature,
Springate and Bergman 2012 (forthcoming).

iHOP – Information Hyperlinked over Proteins

iHOP

:: DESCRIPTION

 iHOP provides fast, accurate, comprehensive, and up-to-date summary information on more than 80,000 biological molecules by automatically extracting key sentences from millions of PubMed documents.

::DEVELOPER

Robert Hoffmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W21-6. Epub 2007 May 7.
iHOP web services.
Fernández JM, Hoffmann R, Valencia A.

PileLine 1.2 / PileLineGUI 1.3 – Handle Genome Position information in Next-generation Sequencing Studies

PileLine 1.2 / PileLineGUI 1.3

:: DESCRIPTION

PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PileLine / PileLineGUI

:: MORE INFORMATION

Citation

PileLine: a toolbox to handle genome position information in next-generation sequencing studies.
Glez-Peña D, Gómez-López G, Reboiro-Jato M, Fdez-Riverola F, Pisano DG.
BMC Bioinformatics. 2011 Jan 24;12:31.

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies.
López-Fernández H, Glez-Peña D, Reboiro-Jato M, Gómez-López G, Pisano DG, Fdez-Riverola F.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W562-6. Epub 2011 Jun 6.

 

 

Endog 4.8 – Analyse Pedigree Information

Endog 4.8

:: DESCRIPTION

ENDOG‘s Primary functions are the computation of the individual inbreeding (F) (Wright, 1931) and the average relatedness (AR) (Gutiérrez et al., 2003; Goyache et al., 2003) coefficients. Additionally, users can compute with ENDOG useful parameters in population genetics such as that described for Biochard et al. (1997) for the number of ancestors explaining genetic variability or those proposed by Robertson (1953) and Vassallo et al. (1996) for the genetic importance of the herds. ENDOG also can compute F statistics (Wright, 1978) from genealogical information following Caballero and Toro (2000; 2002). Moreover, the present version of ENDOG calculates effective population size following different methodologies including regression approaches and particularly the recently proposed realized effective population size from individual increase in inbreeding (Gutiérrez et al., 2008), modified to account for avoidance of self-fertilization (Gutiérrez et al., 2009).

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Endog

:: MORE INFORMATION

Citation

A note on ENDOG: a computer program for analysing pedigree information.
Gutiérrez JP, Goyache F.
J Anim Breed Genet. 2005 Jun;122(3):172-6.

ExtractImputed 0.05 – Extract Information for a Subset of Sites from Imputed Dataset

ExtractImputed 0.05

:: DESCRIPTION

ExtractImputed is a software to extract information for a subset of sites from imputed dataset

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

  ExtractImputed

:: MORE INFORMATION

MICE 1.4 – Mouse Information & Classification Entity

MICE 1.4

:: DESCRIPTION

MICE (Mouse Information and Classification Entity) is a program aimed at facilitating the monitoring of animals in their facility. It consists of a virtual facility in which scientists can perform all the tasks done in the real world (i.e., receiving animals, breeding, etc…). Each animal is recorded with all associated information (birth date, cage number, ID number, tail analysis number, parents, genetic status, genetic background and more), allowing for reliable tracking. Animals can be identified, grouped, sorted, moved…, according to any parameter of interest to the scientist, including associated comments. Crossings are automatically processed by the program, which determines the new genetic background, generation number, cage location and due date.

MICE reminds the user when births are expected, and entering the newborn animals only requires a few clicks (of the mouse!). The genealogy of each animal can be determined in two different ways, including a visual tree from which each ancestor’s information can be retrieved.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

MICE for Win ; for Mac

:: MORE INFORMATION

Citation:

MICE, a program to track and monitor animals in animal facilities. BMC Genetics 2001 Mar;2(1):4

Any comment and/or proposal concerning this application is welcome! Please contact P. Pognonec for additional information.