Tag: Software

PIPS 1.1.2 – Pathogenicity Island Prediction Software

PIPS 1.1.2

:: DESCRIPTION

PIPS is a software developed intending to identify Putative Pathogenicity Islands in pathogenic bacteria integrating the prediction of several algorithms.

::DEVELOPER

Siomar Soares et al.

: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PIPS

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30848. doi: 10.1371/journal.pone.0030848. Epub 2012 Feb 15.
PIPS: pathogenicity island prediction software.
Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R Jr, Mattos-Guaraldi AL, Miyoshi A, Azevedo V.

LINNAEUS 2.0 – Species Name Recognition and Normalization software

LINNAEUS 2.0

:: DESCRIPTION

LINNAEUS is a general-purpose dictionary matching software, capable of processing multiple types of document formats in the biomedical domain (MEDLINE, PMC, BMC, OTMI, text, etc.). It can produce multiple types of output (XML, HTML, tab-separated-value file, or save to a database). It also contains methods for acting as a server (including load balancing across several servers), allowing clients to request matching over a network. A package with files for recognizing and identifying species names is available for LINNAEUS, showing 94% recall and 97% precision compared to LINNAEUS-species-corpus.

::DEVELOPER

the Bergman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 LINNAEUS

:: MORE INFORMATION

Citation

Martin Gerner, Goran Nenadic and Casey M Bergman
LINNAEUS: A species name identification system for biomedical literature
BMC Bioinformatics 2010, 11:85

Models@Home 12.1 – Distributed Computing Software for Protein Modeling

Models@Home 12.1

:: DESCRIPTION

Models@Home is a distributed computing environment . Instead you can run all your favourite programs in parallel, without any need to modify or adapt them. The Models@Home screensaver allows to turn a heterogeneous Windows / Linux network into a uniform cluster.  At the CMBI , Models@Home is used for most protein modeling tasks, all YASARA force fields were developed with computer power provided by Models@Home.

::DEVELOPER

YASARA Biosciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

Models@Home

:: MORE INFORMATION

Citation

E.Krieger & G.Vriend (2002),
“Models@Home: distributed computing in bioinformatics using a screensaver based approach“,
Bioinformatics 18, 315-318.

MetaFIND 0.8 – Java-based Metabolomics Analysis software

MetaFIND 0.8

:: DESCRIPTION

MetaFIND ( Metabolomics Feature INterrogation and Discovery) is a Java-based feature analysis tool that enables real-time, interactive correlation analysis of feature sets, discovery of addtional related features and analysis of related metabolites. It is designed specifically to aid feature analysis within NMR metabolomics data.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Java

:: DOWNLOAD

 MetaFIND

:: MORE INFORMATION

Citation

MetaFIND: a feature analysis tool for metabolomics data.
Bryan K, Brennan L, Cunningham P.
BMC Bioinformatics. 2008 Nov 5;9:470.

GRAST 1.0 – Genome Reduction Analysing Software Tool

GRAST 1.0

:: DESCRIPTION

GRAST allows the user to analyse genome reduction by whole genome comparison between a reduced genome and a reference genome (a close relative to the reduced genome). A number of the options in GRAST can also be used for a whole genome comparison of non-reduced genomes.

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 GRAST

:: MORE INFORMATION

Citation

GRAST: a new way of genome reduction analysis using comparative genomics.
Toft C, Fares MA.
Bioinformatics. 2006 Jul 1;22(13):1551-61. Epub 2006 Apr 6.

Figaro 1.05 – Novel Vector Trimming software

Figaro 1.05

:: DESCRIPTION

Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling short oligonucleotide frequencies within a set of reads, Figaro is able to determine which DNA words are most likely associated with vector sequence.

::DEVELOPER

Figaro Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Figaro

:: MORE INFORMATION

Citation:

James Robert White, Michael Roberts, James A. Yorke and Mihai Pop
Figaro: a novel statistical method for vector sequence removal
Bioinformatics (2008) 24 (4): 462-467.

 

CMC 20100422 – Cross-mapping Correction software

CMC 20100422

:: DESCRIPTION

CMC (Cross-mapping Correction)is a  software of modern high-throughput technologies which enable deep sequencing of non-coding RNA species, such as miRNAs, on an unprecedented scale. When mapping such small RNAs to the genome, cross-mapping may occur, in which RNA sequences originating from one genomic locus are inadvertently mapped to a different locus. This may give rise to spurious novel RNAs, as well as spurious editing sites in known miRNAs. The cross-mapping correction software is a Python script that aims to correct for such cross-mapping effects.

::DEVELOPER

 FANTOM

:: SCREENSHOTS

N/A

::  REQUIREMENTS

:: DOWNLOAD

  CMC

:: MORE INFORMATION

Citation

De Hoon, M.J.L., et al. (2010):
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
Genome Research 20: 257-264 (2010).

Huygens 4.4 – 3D Huygens Deconvolution & Analysis Software

Huygens 4.4

:: DESCRIPTION

Huygens is high quality restoration (deconvolution) and visualization software for microscopists.

::DEVELOPER

Scientific Volume Imaging B.V.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  Huygens

:: MORE INFORMATION

MOIL 12.0.3923 – Molecular Modeling Software

MOIL 12.0.3923

:: DESCRIPTION

MOIL is a package for molecular dynamics and modeling. Moil supports the usual set of tools for molecular modeling by classical mechanics, including energy calculations, energy minimization, molecular dynamics, and more.

::DEVELOPER

MOIL team: Thomas Blom, Peter Majek, Serdal Kirmizialtin, and Ron Elber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • TCL

:: DOWNLOAD

MOIL

:: MORE INFORMATION

Citation

R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker,C. Keasar, J. Zhang and A. Ulitsky
“MOIL: A program for simulations of macromolecules“,
Computer Physics Communications, 91, 159-189(1995)

SPAM 3.7b – Genetic Stock Identification Software

SPAM 3.7b

:: DESCRIPTION

SPAM (Statistics Program for Analysing Mixtures) estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem.

::DEVELOPER

Gene Conservation Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SPAM

:: MORE INFORMATION

Citation

Debevec, Gates, Masuda, Pella, Reynolds, Seeb (2000),
“SPAM (version 3.2): statistics program for analyzing mixtures“,
Journal of Heredity, 91:509-511.

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