DOTcvpSB 2010_E4 – Matlab Toolbox for Dynamic Optimization in Systems Biology

DOTcvpSB 2010_E4

:: DESCRIPTION

DOTcvpSB is a software toolbox which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 DOTcvpSB

:: MORE INFORMATION

Citation:

T. Hirmajer, E. Balsa-Canto and J. R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinformatics 2009, 10:199

SWALO – Scaffolding with Assembly Likelihood Optimization

SWALO

:: DESCRIPTION

SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  •  Bowtie 2

:: DOWNLOAD

SWALO

:: MORE INFORMATION

 

PIVO 2 – Phylogeny by IteratiVe Optimization

PIVO 2

:: DESCRIPTION

PIVO is a program that reconstructs ancestral gene orders on complex phylogenies. Because it uses the DCJ model, it can handle linear, circular, and multilinear genomes. PIVO is mainly targeted at reconstructing rerrangement histories of mitochondrial genomes.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 PIVO

:: MORE INFORMATION

Citation

Albert Herencsár, Broňa Brejová .
An Improved Algorithm for Ancestral Gene Order Reconstruction.
In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies – Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.

GIFT 1.0.0 – Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions

GIFT1.0.0

:: DESCRIPTION

GIFT is a C++ package to infer the chemogenomic features from drug-target interactions.

::DEVELOPER

GIFT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • C++ Compiler

:: DOWNLOAD

 GIFT

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 29. pii: btv181.
Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions.
Zu S, Chen T, Li S

EPISOFT – Epitope Vaccine Optimization Server

EPISOFT

:: DESCRIPTION

EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

::DEVELOPER

Immunomedicine Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines.
Sheikh QM, Gatherer D, Reche PA, Flower DR.
Bioinformatics. 2016 Jul 10. pii: btw399.

CRISPR-DO 0.1 – Genome-wide CRISPR Design and Optimization

CRISPR-DO 0.1

:: DESCRIPTION

CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.

::DEVELOPER

CRISPR-DO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Python

:: DOWNLOAD

 CRISPR-DO

:: MORE INFORMATION

Citation:

CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.

GISMO 2.0 – Gibbs Sampler for Multi-alignment Optimization

GISMO 2.0

:: DESCRIPTION

GISMO is a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA)

::DEVELOPER

GISMO team

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISMO

:: MORE INFORMATION

Citation

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald AF, Altschul SF.
PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936.

COOL – Web-based Multi-objective Optimization platform for Synthetic Gene Design

COOL

:: DESCRIPTION

COOL (Codon Optimization On-Line) can be used to design a nucleotide sequence for improved expression of the desired protein within the target host organism.

::DEVELOPER

Bioinformatics GroupBioprocessing Technology Institute (BTI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • PHP

:: DOWNLOAD

 COOL

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 26.
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design.
Chin JX1, Chung BK, Lee DY.

ATGme – A Simple DNA Sequence Optimization tool

ATGme

:: DESCRIPTION

ATGme is an open-source web-based application which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence.

::DEVELOPER

Edward Daniel & Mirja Krause.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M.
BMC Bioinformatics. 2015 Sep 21;16(1):303. doi: 10.1186/s12859-015-0743-5.

MOSAICS 3.9.2 / PymoSAICS – Methodologies for Optimization and SAmpling In Computational Studies

MOSAICS 3.9.2 / PymoSAICS

:: DESCRIPTION

MOSAICS is a sampling program developed to improve sampling efficiency by incorporating natural move-sets for proteins and nucleic acids.

MOSAICS-EM is a software package designed to refine molecular conformations directly against two-dimensional (2D) electron-microscopy images.

PymoSAICS is a pyMol plugin of MOSAICS.

::DEVELOPER

konrad k.

:: SCREENSHOTS

PymoSAICS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python
  • pyMOL

:: DOWNLOAD

 MOSAICS / PymoSAICS

:: MORE INFORMATION

Citation

Exploring peptide/MHC detachment processes using Hierarchical Natural Move Monte Carlo.
Knapp B, Demharter S, Deane CM, Minary P.
Bioinformatics. 2015 Sep 22. pii: btv502