RNALYZER – RNA Structural Comparison Framework

RNALYZER

:: DESCRIPTION

RNAlyzer is a computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

RNALYZER

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Java3D
  • OpenGL

:: DOWNLOAD

 RNALYZER

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(12):5978-90. doi: 10.1093/nar/gkt318.
RNAlyzer–novel approach for quality analysis of RNA structural models.
Lukasiak P1, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J.

PrePPItar 0.0.1 – Machine Learning Framework to Predict PPI Target for Drug

PrePPItar 0.0.1

:: DESCRIPTION

PrePPItar is a computational method to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs.

::DEVELOPER

ZHANGroup

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 PrePPItar

:: MORE INFORMATION

Citation:

Computational probing protein-protein interactions targeting small molecules.
Wang YC, Chen SL, Deng NY, Wang Y.
Bioinformatics. 2015 Sep 28. pii: btv528.

OpenMS / TOPP / TOPPAS 2.0.0 – C++ Framework for Proteomics

OpenMS / TOPP / TOPPAS 2.0.0

:: DESCRIPTION

OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.

 TOPP (The OpenMS Proteomics Pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. We are currently at well over 40 tools, covering everything from basic signal processing of MS data, to wrapping MS/MS search engines, map alignment, retention time prediction, identification mapping/filtering and much more.

TOPPAS (The TOPP Pipeline Assistant ) is a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction thus reduces to simple drag-and-drop of analysis tools and adding connections in between. As building blocks, you can use all TOPP tools and UTILS shipped with OpenMS. Additionally we provide wrappers for external tools. To add your own external tool, all you need to do is to write a little script.

DEVELOPER

OpenMS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows  / MacOsX
  • C++ Compiler

:: DOWNLOAD

 OpenMS / TOPP / TOPPAS

:: MORE INFORMATION

Citation:

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data.
Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.
J Proteome Res. 2012 Jul 6;11(7):3914-20. Epub 2012 May 24.

OpenMS and TOPP: open source software for LC-MS data analysis.
Bertsch A, Gröpl C, Reinert K, Kohlbacher O.
Methods Mol Biol. 2011;696:353-67.

Frida 1.1.0 – FRamework for Image Dataset Analysis

Frida 1.1.0

:: DESCRIPTION

Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.

::DEVELOPER

JHU Tissue MicroArray Core Facility

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

Frida

:: MORE INFORMATION

Citation:

Cornish T, Morgan J, Gurel B, and De Marzo AM.
FrIDA: An open source framework for image dataset analysis.
Arch. Pathol. Lab. Med. 132:856 (2008). Originally presented at Advancing Practice, Instruction and Innovation Through Informatics: Pittsburgh, PA, 2007.

SpRay 1.1 – Scalable Visual Analytics Framework for High Dimensional data

SpRay 1.1

:: DESCRIPTION

SpRay supports the visualization of the high dimensional data; such as microarray data using parallel coordinates and information visualization methods.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOS
  • R package

:: DOWNLOAD

SpRay

:: MORE INFORMATION

ALF 1.0 – Simulation Framework for Genome Evolution

ALF 1.0

:: DESCRIPTION

ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.

::DEVELOPER

CBRG– Computational Biochemistry Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Mac /  Linux

:: DOWNLOAD

 ALF

:: MORE INFORMATION

Citation

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz:
ALF – A Simulation Framework for Genome Evolution.
Mol Biol Evol, 29(4):1115-1123, April 2012.

OpenStructure 1.4.0 – Computational Structural Biology Framework

OpenStructure 1.4.0

:: DESCRIPTION

OpenStructure is an open-source computational structural biology framework.This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OS X

:: DOWNLOAD

 OpenStructure

:: MORE INFORMATION

Citation

M. Biasini, V. Mariani, J. Haas, S. Scheuber, A.D. Schenk, T. Schwede and A. Philippsen
OpenStructure: A flexible software framework for computational structural biology,
Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481.

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):701-9. doi: 10.1107/S0907444913007051. Epub 2013 Apr 19.
OpenStructure: an integrated software framework for computational structural biology.
Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, Johner N, Schenk AD, Philippsen A, Schwede T.

MicroPreP – Microarray data Preprocessing framework

MicroPreP

:: DESCRIPTION

MicroPreP framework was developed to provide a pipeline to transform raw intensity data from cDNA microarrays into high-quality data

::DEVELOPER

Anne de Jong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MicroPreP

:: MORE INFORMATION

Citation

Appl Bioinformatics. 2003;2(4):241-4.
MicroPreP: a cDNA microarray data pre-processing framework.
van Hijum SA, García de la Nava J, Trelles O, Kok J, Kuipers OP.

DNENRICH – A framework for Calculating Recurrence and Gene-set Enrichment for de novo Mutations

DNENRICH

:: DESCRIPTION

DNENRICH is a statistical software package for calculating gene set enrichment for de novo mutations (typically detected by exome sequencing) of a disease cohort.

::DEVELOPER

Menachem Fromer and Shaun Purcell at the Center for Statistical Genetics at the Icahn School of Medicine at Mount Sinai.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Complier

:: DOWNLOAD

  DNENRICH

:: MORE INFORMATION

Citation

Fromer et al. (2014)
De novo mutations in schizophrenia implicate synaptic networks.
Nature 506(7487):179-84.

DSM 20140113 – Distributed String Mining Framework

DSM 20140113

:: DESCRIPTION

DSM framework is a software of content-based exploration and retrieval method for whole metagenome sequencing samples.

:: DEVELOPER

DSM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 DSM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 19. pii: btu340. [Epub ahead of print]
Exploration and retrieval of whole-metagenome sequencing samples.
Seth S, Välimäki N, Kaski S, Honkela A.