BAMTOOLS 2.5.1 – C++ API and Toolkit for Analyzing and Managing BAM files

BAMTOOLS 2.5.1

:: DESCRIPTION

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BAMTOOLS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1691-2. Epub 2011 Apr 14.
BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, , Strömberg MP, Marth GT.

openBIS 14.12.1/ openBIS ELN-LIMS – Managing Biological Information

openBIS 14.12.1 / openBIS ELN-LIMS

:: DESCRIPTION

openBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata.

The aim of openBIS ELN-LIMS was to create a stable database with an intuitive and simple-to-use graphical user interface (GUI) where all relevant lab data can be collected.

::DEVELOPER

The Center for Information Sciences and Databases (CISD)

:: SCREENSHOTS

n/a

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • JRE
  • PostgreSQL

:: DOWNLOAD

  openBIS , openBIS ELN-LIMS

:: MORE INFORMATION

Citation

openBIS ELN-LIMS: an open-source database for academic laboratories.
Barillari C, Ottoz D, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F.
Bioinformatics. 2015 Oct 27. pii: btv606

BMC Bioinformatics. 2011 Dec 8;12:468. doi: 10.1186/1471-2105-12-468.
openBIS: a flexible framework for managing and analyzing complex data in biology research.
Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstr?m L, Aebersold R, Rinn B

mSpecs Editor 1.01 – Tool for Managing Mass Spectral Libraries

mSpecs Editor 1.01

:: DESCRIPTION

mSpecs Editor is a free tool for managing mass spectral libraries with an additional focus on gas chromatography / mass spectrometry, liquid chromatography / mass spectrometry and related techniques.

::DEVELOPER

Bernhard Thielen , bernhard.thielen@googlemail.com

:: SCREENSHOTS

mSpecsEditor

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 mSpecs Editor

:: MORE INFORMATION

Citation

Thielen B, Heinen S, Schomburg D:
mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics.
BMC Bioinformatics. 2009 Jul 22;10:229

GSCANDB 1.0 – Portable System for Managing and Viewing Genome Scan Data

GSCANDB 1.0

:: DESCRIPTION

GSCANDB is a portable system for managing and viewing genome scan data.

::DEVELOPER

Richard Mott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • Perl-CGI
  • Apache
  • JAVA
  • ANT

:: DOWNLOAD

 GSCANDB

:: MORE INFORMATION

Citation

Taylor M, Valdar W, Kumar A, Flint J, Mott R.
Management, presentation and interpretation of genome scans using GSCANDB.
Bioinformatics. 2007 Jun 15;23(12):1545-9. Epub 2007 Mar 30.

PLAN 1.0 RC19 – High-throughput BLAST Searches and Managing and Mining Results

PLAN 1.0 RC19

:: DESCRIPTION

PLAN (Personal BLAST Navigator) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

:: DOWNLOAD

 PLAN

:: MORE INFORMATION

Citation:

He, J., Dai, X. and Zhao, X. (2007).
PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results.
BMC Bioninformatics 8:53.