myPhyloDB v.1.1.2 – A Local Web Server for the Storage and Analysis of Metagenomic Data

myPhyloDB v.1.1.2

:: DESCRIPTION

myPhyloDB is an open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory’s microbial ecology data.

::DEVELOPER

Daniel Manter

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Python

:: DOWNLOAD

 myPhyloDB

:: MORE INFORMATION

Citation

myPhyloDB: a local web server for the storage and analysis of metagenomic data.
Manter DK, Korsa M, Tebbe C, Delgado JA.
Database (Oxford). 2016 Mar 28;2016. pii: baw037. doi: 10.1093/database/baw037.

StatsDB 1.1 – Storage and Understanding of Next Generation Sequencing Run Metrics

StatsDB 1.1

:: DESCRIPTION

StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics.

::DEVELOPER

The Genome Analysis Centre (TGAC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Perl
  • Java
  • MySQL

:: DOWNLOAD

 StatsDB

:: MORE INFORMATION

Citation

F1000Research 2014, 2:248 (doi: 10.12688/f1000research.2-248.v2)
StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.
Ramirez-Gonzalez RH, Leggett RM, Waite D, Thanki A, Drou N, Caccamo M, Davey R

Genomedata 1.3.5 – Storage of Multiple Tracks of Numeric data Anchored to Genome

Genomedata 1.3.5

:: DESCRIPTION

Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 Genomedata

:: MORE INFORMATION

Citation:

Hoffman MM, Buske OJ, Noble WS. 2010.
The Genomedata format for storing large-scale functional genomics data.
Bioinformatics, 26(11):1458-1459; doi:10.1093/bioinformatics/btq164

GRS 1.0 – Compression tool for efficient Storage of Genome Re-Sequencing data

GRS 1.0

:: DESCRIPTION

GRS is a novel compression tool for storing and analyzing Genome ReSequencing data. GRS is able to process the genome sequence data without the use of the reference SNPs and other sequence variation information and automatically rebuild the individual genome sequence data using the reference genome sequence.

:: DEVELOPER

Congmao Wang, Shanghai Jiao Tong University plant developmental biology laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRS

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Apr;39(7):e45. doi: 10.1093/nar/gkr009. Epub 2011 Jan 25.
A novel compression tool for efficient storage of genome resequencing data.
Wang C, Zhang D.

RnamlView 1.0 – Manipulation, Storage & Visualisation of RNA Data

RnamlView 1.0

:: DESCRIPTION

RnamlView is a visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView (above). The application generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.

::DEVELOPER

Fabrice Jossinet, & Eric Westhof, Institut de biologie moleculaire et cellulaire du CNRS

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnamlView

:: MORE INFORMATION

Citation

Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003).
Tools for the automatic identification and classification of RNA base pairs.
Nucleic Acids Research 31.13: 3450-3460.

WIST 1.1 – The Workflow Information Storage Toolkit

WIST 1.1

:: DESCRIPTION

WIST is a template-based toolkit to facilitate rapid LIMS (Laboratory Information Management System) development. WIST is designed to create LIMS modules with a web-based front end and a SQL database back end, along with a repository for larger data objects (e.g., files) that are impractical to store in SQL tables.

::DEVELOPER

The VIMSS (Virtual Institute of Microbial Stress and Survival)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Apach
  • MySQL
  • Perl

:: DOWNLOAD

 WIST

:: MORE INFORMATION

Citation

WIST: toolkit for rapid, customized LIMS development.
Huang YW, Arkin AP, Chandonia JM.
Bioinformatics. 2011 Feb 1;27(3):437-8. doi: 10.1093/bioinformatics/btq676. Epub 2011 Jan 21.

Prometheus 0.8.0 – Storage, Management, and Analysis of Fermentation data

Prometheus 0.8.0

:: DESCRIPTION

Prometheus is a versatile software platform for the storage, management, and analysis of fermentation data. The multi application system allows storing of arbitrary online and offline parameters and supports gene expression studies by including existing applications for microarray and qPCR analysis. The newly developed application Prometheus features data import, runtime chart generation, data statistics, and a versatile data export mechanism. The platform can be accessed using a web browser and exposes many functions as a web service. The complete system is protected by a user management system providing single sign on and fine grained data sharing mechanisms.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 Prometheus

:: MORE INFORMATION

Citation

Rader R, Pabinger S, Specht T, Ramsauer T, Trajanoski Z.
Prometheus: Integrating bioprocess and gene expression data for industrial bioprocess optimization.
submitted

Ebbie 3.0.9 – Analysis & Storage of Small RNA Cloning Data

Ebbie 3.0.9

:: DESCRIPTION

Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases.

::DEVELOPER

H Alexander Ebhardt

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Ebbie

:: MORE INFORMATION

Citation

H Alexander Ebhardt , Kay C Wiese and Peter J Unrau
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
BMC Bioinformatics 2006, 7:185doi:10.1186/1471-2105-7-185

maxd 2.0 – Storage & Analysis of Microarray Data

maxd 2.0

:: DESCRIPTION

maxd is a data warehouse and visualisation environment for genomic expression data.maxd is made up of two software components:

maxdLoad2, for data storage, annotation and export,

maxdView, for data visualisation and analysis.

::DEVELOPER

Microarray Bioinformatics Group at the University of Manchester

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Max OS X
  • JAVA

:: DOWNLOAD

maxd

:: MORE INFORMATION

The software is released under the terms of the Perl Artistic Licence .