Tag: Library

LibSBMLSim 1.4.0 – The library for Simulating SBML models

LibSBMLSim 1.4.0

:: DESCRIPTION

LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.

::DEVELOPER

Funahashi Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LibSBMLSim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157.
LibSBMLSim: A reference implementation of fully functional SBML simulator.
Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

PD5 1.5 – Software Library for the Development of Primer Design Applications

PD5 1.5

:: DESCRIPTION

PD5 is a C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

PD5 Online Version

::DEVELOPER

 the Bioinformatics group in the Department of Computer Science at Aberystwyth University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • C++ Compiler

:: DOWNLOAD

 PD5

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e80156. doi: 10.1371/journal.pone.0080156.
PD5: A General Purpose Library for Primer Design Software.
Riley MC, Aubrey W, Young M, Clare A.

ScalaBLAST 2.4.53 – Multiprocessor Implementation of the NCBI BLAST library

ScalaBLAST 2.4.53

:: DESCRIPTION

ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. ScalaBLAST supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, or XML).

:: DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • gcc
  • MPI

:: DOWNLOAD

 ScalaBLAST

:: MORE INFORMATION

Citation

Oehmen, C.S. and J. Nieplocha. 2006.
“ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis“,
IEEE Transactions on Parallel and Distributed Systems, 17(8): 740-749.

Bioinformatics. 2013 Mar 15;29(6):797-8. doi: 10.1093/bioinformatics/btt013. Epub 2013 Jan 29.
ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems.
Oehmen CS, Baxter DJ.

VaLiAnT – Variant Library Annotation Tool

VaLiAnT

:: DESCRIPTION

VaLiAnT is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments.

::DEVELOPER

CASM IT

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

VaLiAnT

:: MORE INFORMATION

Citation

Barbon L, Offord V, Radford EJ, Butler AP, Gerety SS, Adams DJ, Tan HK, Waters AJ.
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments.
Bioinformatics. 2021 Nov 16:btab776. doi: 10.1093/bioinformatics/btab776. Epub ahead of print. PMID: 34791067.

PrIME 1.0.5 – Library and Accompanying tools for Phylogenetics

PrIME 1.0.5

:: DESCRIPTION

PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PrIME

:: MORE INFORMATION

Citation:

Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044

BN++ 1.1 – Biochemical Network Library

BN++ 1.1

:: DESCRIPTION

BN++ (formerly known as ‘BioMiner’) is a software system in C++ for analyzing and visualizing complex biochemical networks and processes. BN++ was designed to simplify the implementation of tools for answering a broad range of interesting biochemical questions. BN++ is based on a new comprehensive, extensible and reusable data model capable of representing complex and diverse biochemical data in a unified fashion.

DEVELOPER

the Chair for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows  / MacOsX
  • C++ Compiler

:: DOWNLOAD

 BN++

:: MORE INFORMATION

Citation:

Küntzer J, Blum T, Gerasch A, Backes C, Hildebrandt A, Kaufmann M, Kohlbacher O, Lenhof HP:
BN++ -A Biological Information System.
J Integr Bioinformatics 2006, 3(2):34.

BiblioSpec 2.0 – Creat and Search MS/MS Peptide Spectrum Libraries

BiblioSpec 2.0

:: DESCRIPTION

BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BiblioSpec

:: MORE INFORMATION

Citation

Using BiblioSpec for creating and searching tandem MS peptide libraries.
Frewen B, MacCoss MJ.
Curr Protoc Bioinformatics. 2007 Dec;Chapter 13:Unit 13.7.

Bioclojure – Functional Library for the Manipulation of Biological Sequences

Bioclojure

:: DESCRIPTION

BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.

::DEVELOPER

Bioclojure team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BioClojure

:: MORE INFORMATION

Citation

Bioclojure: a functional library for the manipulation of biological sequences.
Plieskatt J, Rinaldi G, Brindley PJ, Jia X, Potriquet J, Bethony J, Mulvenna J.
Bioinformatics. 2014 May 2. pii: btu311

GHMM 0.9 – General Hidden Markov Model library

GHMM 0.9

:: DESCRIPTION

The GHMM is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GHMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Nov 2;12:428.
Fast MCMC sampling for hidden Markov Models to determine copy number variations.
Mahmud MP, Schliep A.

 

BioJS 2.0 – A library of JavaScript Components to Represent Biological Data

BioJS 2.0

:: DESCRIPTION

BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers.

::DEVELOPER

BioJS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BioJS

:: MORE INFORMATION

Citation

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics. 2013 Apr 15;29(8):1103-4.