BRISK – Biology-Related Information Storage Kit

BRISK

:: DESCRIPTION

BRISK is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists.

::DEVELOPER

Genapha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • MySQL

:: DOWNLOAD

   BRISK

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 1;27(17):2422-5. doi: 10.1093/bioinformatics/btr389. Epub 2011 Jun 27.
BRISK–research-oriented storage kit for biology-related data.
Tan A, Tripp B, Daley D.

GWIPS-viz – Genome Wide Information on Protein Synthesis

GWIPS-viz

:: DESCRIPTION

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique

::DEVELOPER

GWIPS-viz team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2015 Mar 3. doi: 10.1002/pmic.201400603.
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
Michel AM1, Ahern AM, Donohue CA, Baranov PV.

Uniprot DAT File Parser 1.1.5674 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5674

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION

MetaCrop 2.0 – Browsing and Working with Information from the MetaCrop database

MetaCrop 2.0

:: DESCRIPTION

MetaCrop is an Add-on to enable browsing of the content of the handcurated Metacrop database. Users can directly load hand-layouted pathway maps or metabolic network models to use for browsing, pathway exploration, data-mapping and analysis or use them for metabolic modelling. The user can also filter the pathway for species specific information, which will be visually highlighted.

::DEVELOPER

Chair for Life Science Informatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D1173-7. Epub 2011 Nov 15.
MetaCrop 2.0: managing and exploring information about crop plant metabolism.
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S.

MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Jiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

HBN – Integration of Relational and Hierarchical Network Information for Protein Function Prediction

HBN

:: DESCRIPTION

HBN is a software of hierarchical binomial neighborhood (HBN) method for Protein Function Prediction

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 HBN

:: MORE INFORMATION

Citation

Jiang, X., Nariai, N., Steffen, M., Kasif, S., and Kolaczyk, E.D. (2007).
Integration of Relational and Hierarchical Network Information for Protein Function Prediction.
BMC Bioinformatics, 9:350.

Meta-All 1.2 – Store and Access Information about Metabolic Pathways

Meta-All 1.2

:: DESCRIPTION

Meta-All is a software that allows to store and access information about metabolic pathways, including reaction kinetics, detailed locations, environmental circumstances and taxonomic information.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Meta-All

:: MORE INFORMATION

Citation

S. Weise, I. Grosse, C. Klukas, D. Koschuetzki, U. Scholz, F. Schreiber and B.H. Junker.
Meta-All: a system for managing metabolic pathway information.
BMC Bioinformatics, 7:e465, 2006.

AlphaPred – Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information

AlphaPred

:: DESCRIPTION

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur H & Raghava GP. (2004).
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
Proteins. 55: 83-90