MEIGO / MEIGO-M 20140703 / MEIGO-R 0.99.6 / pymeigo 1.0.0 – MEtaheuristics for bIoinformatics Global Optimization

MEIGO / MEIGO-M 20140703 / MEIGO-R 0.99.6 / pymeigo 1.0.0

:: DESCRIPTION

MEIGO is a global optimization toolbox that includes a number of metaheuristic methods as well as (currently in the R version only) a Bayesian inference method for parameter estimation

MEIGO-M (Matab version)

MEIGO-R (R version)

pymeigo is a python package that provides a python interface to the optimisation tool MEIGOR

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • R/ MatLab/ Python

:: DOWNLOAD

MEIGO-M / MEIGO-R / pymeigo

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136.
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR1, Saez-Rodriguez J.

BioDWH 0.2 – Bioinformatics Data Warehouse

BioDWH 0.2

:: DESCRIPTION

BioDWH is a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. It stands out from other approaches by providing up-to-date integrated knowledge, platform and database independence as well as high usability and customization.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java
  • Oracle or MySQL

:: DOWNLOAD

 BioDWH

:: MORE INFORMATION

Citation

BioDWH: a data warehouse kit for life science data integration.
Töpel T, Kormeier B, Klassen A, Hofestädt R.
J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-93.

bellmansgap 20150520 – Dynamic Programming for Bioinformatics

bellmansgap 20150520

:: DESCRIPTION

Bellman’s GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique.

::DEVELOPER

Stefan Janssen , Dr. Georg Sauthoff

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 bellmansgap

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):551-60. doi: 10.1093/bioinformatics/btt022. Epub 2013 Jan 25.
Bellman’s GAP–a language and compiler for dynamic programming in sequence analysis.
Sauthoff G1, Möhl M, Janssen S, Giegerich R.

ECplot v2.0 – Making Standardized Plots from large datasets for Bioinformatics Publications

ECplot v2.0

:: DESCRIPTION

ECplot is an online tool for plotting charts from large datasets. This tool supports a variety of chart types commonly used in bioinformatics publications.

::DEVELOPER

Kevin Yuk-Lap Yip

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ECplot 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1467-8. doi: 10.1093/bioinformatics/btu038. Epub 2014 Jan 24.
ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications.
Fok AC1, Mok SS, Lee SD, Yip KY.

SEQ v0.9.4 – Language for Bioinformatics

SEQ v0.9.4

:: DESCRIPTION

SEQ is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

SEQ

:: MORE INFORMATION

Citation:

Ariya Shajii et al.
Seq: a high-performance language for bioinformatics
Proceedings of the ACM on Programming LanguagesOctober 2019 Article No.: 125 https://doi.org/10.1145/3360551

JABAWS 2.2 – JAva Bioinformatics Analysis Web Services

JABAWS 2.2

:: DESCRIPTION

JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview. JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Ronn and GlobPlot; and calculation of amino acid alignment conservation with AACon.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ Amazon EC2
  • Java

:: DOWNLOAD

 JABAWS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2001-2. doi: 10.1093/bioinformatics/btr304. Epub 2011 May 18.
Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA.
Troshin PV, Procter JB, Barton GJ.

Mockrobiota – Public Resource for Microbiome Bioinformatics Benchmarking

Mockrobiota

:: DESCRIPTION

Mockrobiota is a public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

::DEVELOPER

Caporaso Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

Mockrobiota

:: MORE INFORMATION

Citation

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.
Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.
mSystems. 2016 Oct 18;1(5). pii: e00062-16

scikit-bio 0.5.5 – Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics

scikit-bio 0.5.5

:: DESCRIPTION

scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

scikit-bio

:: MORE INFORMATION

UGENE 33.0 – Integrated Bioinformatics Tools

UGENE 33.0

:: DESCRIPTION

UGENE is a visual environment for biomolecular research, integrating ever-growing set of bioinformatics algorithms.

::DEVELOPER

UniPro

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 UGENE 

:: MORE INFORMATION

Citation

Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team.
Bioinformatics. 2012 Apr 15;28(8):1166-7. doi: 10.1093/bioinformatics/bts091. Epub 2012 Feb 24.

NCBI C++ Toolkit 22.0 – Collection of C++ Modules for Bioinformatics

NCBI C++ Toolkit 22.0

:: DESCRIPTION

NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications. NCBI C++ Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NCBI C++ Toolkit

:: MORE INFORMATION

Citation

The NCBI C++ Toolkit Book [Internet].
Vakatov D, editor.