Tag: Open Source

MOSGA 2 – Modular Open-Source Genome Annotator

MOSGA 2

:: DESCRIPTION

The MOSGA is a pipeline that easily creates draft genome annotation by a graphical user interface. It combines several specific prediction tools and generates a submission-ready annotation file.

::DEVELOPER

MOSGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MOSGA

:: MORE INFORMATION

Citation

Martin R, Hackl T, Hattab G, Fischer MG, Heider D.
MOSGA: Modular Open-Source Genome Annotator.
Bioinformatics. 2021 Apr 1;36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003. PMID: 33258916.

Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D.
MOSGA 2: Comparative genomics and validation tools.
Comput Struct Biotechnol J. 2021 Sep 28;19:5504-5509. doi: 10.1016/j.csbj.2021.09.024. PMID: 34712396; PMCID: PMC8517542.

 

Tuftsviewer / Molli 0.99 – Cross Platform Open Source PDB Viewer

Tuftsviewer / Molli 0.99

:: DESCRIPTION

TuftsViewer is an open source program that allows the visualization, rotation and coordinated viewing of multiple 3D protein molecules on the 2D screen.

TuftsViewer has been renamed to Molli. Molli is an open source cross-platform protein structure viewer based on the OpenGL and wxWidgets libraries.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

tuftsviewer

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Molli

:: MORE INFORMATION

Citation:

Matt Menke, Sara Su, Connor Gramazio, Caitlin Crumm, Daniela Extrum-Fernandez and Lenore Cowen,
TuftsViewer: An Intuitive Interface for viewing 3D Protein Structures,
Proceedings of ISMB 3DSIG, p. 24.

PathBuilder 1.0 – open source Software for Annotating and Developing Pathway Resources

PathBuilder 1.0

:: DESCRIPTION

PathBuilder is an open source software to annotate biological information pertaining to signaling pathways and, with minimal additional effort, to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or automatic methods.

::DEVELOPER

The Pandey Lab

:: SCREENSHOTS

PathBuilder

:: REQUIREMENTS

  • Linux / MacOsX /Windows
  • Zope
  • MySQL
  • Python

:: DOWNLOAD

   PathBuilder

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2860-2. doi: 10.1093/bioinformatics/btp453.
PathBuilder–open source software for annotating and developing pathway resources.
Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A.

BioUML 0.9.10 – Open Source Java Framework for Systems Biology

BioUML 0.9.10

:: DESCRIPTION

BioUML is open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data.

::DEVELOPER

BioUML Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 BioUML

:: MORE INFORMATION

Citation

Adv Exp Med Biol. 2012;736:235-45. doi: 10.1007/978-1-4419-7210-1_13.
A modular model of the apoptosis machinery.
Kutumova EO1, Kiselev IN, Sharipov RN, Lavrik IN, Kolpakov FA.

aroma.affymetrix 3.2.0 – Open-source R framework for your Microarray Analysis

aroma.affymetrix 3.2.0

:: DESCRIPTION

Aroma.affymetrix is an R package for analyzing large Affymetrix data sets.  It allows you to analyze 100-1,000s of arrays of various chip types, e.g. expression arrays, SNP chips, exon arrays and so on.

::DEVELOPER

Henrik Bengtsson et al. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package

:: DOWNLOAD

 aroma.affymetrix

:: MORE INFORMATION

Citation

ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
Ortiz-Estevez M, Bengtsson H, Rubio A.
Bioinformatics. 2010 Aug 1;26(15):1827-33. doi: 10.1093/bioinformatics/btq300

Estimation and assessment of raw copy numbers at the single locus level.
Bengtsson H, Irizarry R, Carvalho B, Speed TP.
Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016.

InterMine 5.0.3 – Open Source Biological Data Warehouse System

InterMine 5.0.3

:: DESCRIPTION

InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data.InterMine enables the creation of biological databases accessed by sophisticated web query tools.

::DEVELOPER

the Micklem lab at the University of Cambridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server
  • Java
  • PostgreSQL
  • TomCat
  • Perl

:: DOWNLOAD

 InterMine

:: MORE INFORMATION

Citation

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.
Bioinformatics. 2012 Dec 1;28(23):3163-5. doi: 10.1093/bioinformatics/bts577.

IOCBio 1.2.2 – Open-source Software from the Laboratory of Systems Biology

IOCBio 1.2.2

:: DESCRIPTION

The IOCBio project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

IOCBio

:: MORE INFORMATION

Citation

J Microsc. 2011 Aug;243(2):124-40. doi: 10.1111/j.1365-2818.2011.03486.x. Epub 2011 Feb 15.
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images.
Laasmaa M, Vendelin M, Peterson P.

YouScope 2.1.0 – Open-source Microscope Control software

YouScope 2.1.0

:: DESCRIPTION

YouScope is a free, open-source microscope control software compatible with most present-day automized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

YouScope

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 YouScope

:: MORE INFORMATION

Citation

Curr Protoc Mol Biol. 2012 Apr;Chapter 14:Unit 14.21.1-23. doi: 10.1002/0471142727.mb1421s98.
Use of YouScope to implement systematic microscopy protocols.
Lang M, Rudolf F, Stelling J.

Bioconductor 3.13 – Open Source Software for Bioinformatics

Bioconductor 3.13

:: DESCRIPTION

Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

::DEVELOPER

Bioconductor Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bioconductor

:: MORE INFORMATION

Publications

SeqAn 2.4.0 – Open Source C++ Library of Sequences Analysis

SeqAn 2.4.0

:: DESCRIPTION

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

::DEVELOPER

SeqAn Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 SeqAn

:: MORE INFORMATION

Citation

SeqAn an efficient, generic C++ library for sequence analysis.
Döring A, Weese D, Rausch T, Reinert K.
BMC Bioinformatics. 2008 Jan 9;9:11.