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.

miRanda 1.9 – microRNA Target Detection Software

miRanda 1.9

:: DESCRIPTION

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. miRanda reads RNA sequences (such as microRNAs) from file1 and genomic DNA/RNA sequences from file2. Both of these files should be in FASTA format.

::DEVELOPER

the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

miRanda

:: MORE INFORMATION

Citation

John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS.,
Human MicroRNA Targets
PLoS Biol. 2005 Jul;3(7):e264.

PeakQuant 1.5.47 – Proteomics Software Suit

PeakQuant 1.5.47

:: DESCRIPTION

PeakQuant (formerly known as Peakardt) serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

PeakQuant

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 PeakQuant

:: MORE INFORMATION

Citation

OMICS. 2012 Sep;16(9):457-67. doi: 10.1089/omi.2011.0140. Epub 2012 Aug 21.
Find pairs: the module for protein quantification of the PeakQuant software suite.
Eisenacher M1, Kohl M, Wiese S, Hebeler R, Meyer HE, Warscheid B, Stephan C.

TreeView X 0.5-1 – Tree Drawing Software

TreeView X 0.5-1

:: DESCRIPTION

TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the version of TreeView available for the Mac Classic and Windows

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 TreeView X

:: MORE INFORMATION

Citation

Page, R. D. M. 1996.
TREEVIEW: An application to display phylogenetic trees on personal computers.
Computer Applications in the Biosciences 12: 357-358.

GenomeTools 1.6.2 – Genome Analysis Software

GenomeTools 1.6.2

:: DESCRIPTION

GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

::DEVELOPER

GenomeTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows with Cygwin

:: DOWNLOAD

GenomeTools

The GenomeTools distribution includes several published software tools:

  • ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
    D. Ellinghaus, S. Kurtz, and U. Willhoeft.
    LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
    BMC Bioinformatics 2008, 9:18
  • tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
    S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
    A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
    BMC Genomics 2008, 9:517
  • uniquesub, a program for computing minimum unique substrings.
    S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
    Optimized design and assessment of whole genome tiling arrays.
    Bioinformatics 2007, 23(13):i195–i204
  • AnnotationSketch, a library for drawing genome annotations.
    S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
    AnnotationSketch: a genome annotation drawing library.
    Bioinformatics 2009, 25(4):533–534
  • ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
    S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
    Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
    Nucleic Acids Research 2009, 37(21):7002–7013
  • MetaGenomeThreader, a software to predict genes, such as PCS’s (predicted coding sequences) in sequences of metagenome projects.
    D.J. Schmitz-Hübsch and S. Kurtz.
    MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
    In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
  • GtEncseq, a compressed biosequence representation with many features.
    S. Steinbiss and S. Kurtz.
    A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
  • Readjoiner, a sequence assembler based on the assembly string graph framework.
    G. Gonnella and S. Kurtz.
    Readjoiner: a fast and memory efficient string graph-based sequence assembler.
    BMC Bioinformatics 2012, 13:82

Bosque 2.0.2 – Phylogenetic Analysis Software

Bosque 2.0.2

:: DESCRIPTION

Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server  can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bosque

:: MORE INFORMATION

Citation:

Ramírez-Flandes S. & O. Ulloa(2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541; doi: 10.1093/bioinformatics/btn466

PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

BioBlender 1.0 – Software built on the Open-source 3D Modeling software Blender

BioBlender 1.0

:: DESCRIPTION

BioBlender is a open source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.

::DEVELOPER

the SciVis Group of the Institute of Clinical Physiology – CNR, Italy.

:: SCREENSHOTS

BioBlender

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

 BioBlender

:: MORE INFORMATION

Citation

Andrei R.M. et al.
Intuitive representation of surface properties of biomolecules using BioBlender.
BMC Bioinformatics 2012, 13(Suppl 4):S16. Published: 28 March 2012

Mason 0.1.2 – Read Simulator software for Illumina, 454 and Sanger reads

Mason 0.1.2

:: DESCRIPTION

Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.

::DEVELOPER

Manuel Holtgrewe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX /Windows

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

Holtgrewe, M. (2010).
Mason – a read simulator for second generation sequencing data.
Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin.

newDNA-Prot – DNA Binding Protein Predict Software

newDNA-Prot

:: DESCRIPTION

newDNA-Prot will predict the DNA-binding proteins when input a protein sequence (Fasta format).

::DEVELOPER

newDNA-Prot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • fortran-windows

:: DOWNLOAD

newDNA-Prot

:: MORE INFORMATION

Citation

newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J.
Comput Biol Chem. 2014 Oct;52:51-9. doi: 10.1016/j.compbiolchem.2014.09.002.