PubSearch 0.8.1 – Literature Curation Management System

PubSearch 0.8.1

:: DESCRIPTION

PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation.

::DEVELOPER

PubSearch Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PubSearch

:: MORE INFORMATION

Citation

Yoo, D, Xu, I, Berardini, T, Rhee, S, Narayanasamy, V, Twigger, S (2006)
PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature..
Curr Protoc Bioinformatics. 2006 Mar;Chapter 9:Unit9.7.

Taverna 2.5 – Workflow Management System

Taverna 2.5

:: DESCRIPTION

Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community.

::DEVELOPER

Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Taverna

:: MORE INFORMATION

Citation:

D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. Pocock, P. Li, and T. Oinn,
Taverna: a tool for building and running workflows of services.,”
Nucleic Acids Research, vol. 34, iss. Web Server issue, pp. 729-732, 2006.

T. Oinn, M. Greenwood, M. Addis, N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M. Pocock, M. Senger, R. Stevens, A. Wipat, and C. Wroe,
Taverna: lessons in creating a workflow environment for the life sciences,
Concurrency and Computation: Practice and Experience, vol. 18, iss. 10, pp. 1067-1100, 2006.

Jflow 1.2 – A Workflow Management System for Web Applications

Jflow 1.2

:: DESCRIPTION

Jflow is a JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and monitor workflows.

::DEVELOPER

Jflow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript
  • Python

:: DOWNLOAD

 Jflow

:: MORE INFORMATION

Citation

Jflow: a workflow management system for web applications.
Mariette J, Escudié F, Bardou P, Nabihoudine I, Noirot C, Trotard MS, Gaspin C, Klopp C.
Bioinformatics. 2015 Oct 10. pii: btv589

SIMS 2.14 – Sample Information Management System

SIMS 2.14

:: DESCRIPTION

SIMS (SIMBioMS) is a web based system that allows researchers to track information related to sample collection, processing, location, transportation and storage conditions etc. The system can be easilly used either for Data submission – entering and editing the information on samples and individuals, or Data access – browsing and querying this information, and generating reports. The organization of data within SIMS is based on three main categories: First level (Persons), Second level (Samples) and Third level (Aliquots), where an arbitrary number of second level records (samples) can be associated with each record from the first level (person) and an arbitrary number of third level records (aliquots) can be associated with each the second level record (sample). It is possible to configure SIMS with other categories’ titles and meta-data (for example, Persons, Vists and Samples or Persons, Characteristics and Samples).

::DEVELOPER

SIMS Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SIMS

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Oct 15;25(20):2768-9. doi: 10.1093/bioinformatics/btp420. Epub 2009 Jul 24.
A System for Information Management in BioMedical Studies–SIMBioMS.
Krestyaninova M1, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.

SBEAMS 0.22.1 – Systems Biology Experiment Analysis Management System

SBEAMS 0.22.1

:: DESCRIPTION

SBEAMS is a framework for collecting, storing, and accessing data produced by a wide variety of experiments. The software provides a customizable framework to meet the needs of modern systems biology research.

SBEAMS – Microarray provides MIAME-compliant Affymetrix GeneChip microarray database functionality under the SBEAMS framework.

SBEAMS-Proteomics is part of the SBEAMS (Systems Biology Experiment Analysis Management System) Project, which is a framework for collecting, storing, and accessing data produced by a variety of different experiments; these experiments can be managed separately but then correlated later under the same framework.

::DEVELOPER

SBEAMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • MySQL

:: DOWNLOAD

  SBEAMS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jun 6;7:286.
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T.

RAMPART 0.12.2 – A Workflow Management System for de novo Genome Assembly

RAMPART 0.12.2

:: DESCRIPTION

RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RAMPART

:: MORE INFORMATION

Citation

RAMPART: a workflow management system for de novo genome assembly.
Mapleson D, Drou N, Swarbreck D.
Bioinformatics. 2015 Jan 30. pii: btv056.

PIMS 4.4.0 – Protein Information Management System

PIMS 4.4.0

:: DESCRIPTION

PiMS (Protein Information Management System) is a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.

:: DEVELOPER

PIMS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • Web Server
  • java

:: DOWNLOAD

 PIMS

:: MORE INFORMATION

Citation:

Acta Cryst. (2011). D67, 249-260 [ doi:10.1107/S0907444911007943 ]
The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory
Morris C et al.

Labmatica 2.2.3 RC1 – Laboratory Information Management System

Labmatica 2.2.3 RC1

:: DESCRIPTION

Labmatica is a Laboratory Information Management System ( LIMS ). With Labmatica you can: manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. Ready made reports and certificates are included in the distribution. You can easily configure these report templates to your corporate identity.

::DEVELOPER

LIMS at work GmbH

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Labmatica

:: MORE INFORMATION

Buy Labmatica LIMS

CDK-Taverna 2.0.5.4 – Workflow Management System for Cheminformatics

CDK-Taverna 2.0.5.4

:: DESCRIPTION

CDK Taverna project based on the “Pipelining Technology” idea tries to address the advantages of software libraries and sophisticated information systems.The project combines two other open-source projects:

The Taverna workbench as a workflow container.
The Chemistry Development Kit (CDK) as a basic chemo-/bioinformatics library.

::DEVELOPER

CDK-Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CDK-Taverna

:: MORE INFORMATION

Citation:

Kuhn T, Willighagen EL, Zielesny A, Steinbeck S:
CDK-Taverna: an open workflow environment for cheminformatics.
BMC Bioinformatics 2010, 11:159.

AIMS 2.10 – Assay Information Management System

AIMS 2.10

:: DESCRIPTION

AIMS is a web based system that serves as the central repository for experimental data produced by different experimental technologies (genomic, transcriptomic, proteomic, metabolomic data etc). The basic structure of AIMS resemples that of SIMS, with data organized around three main categories: Studies, Experiments and Assays. However the system is designed to be extremely flexible reagrding its configuration, since it is intended for one instance of AIMS system to be used for data obtained by several different technologies.

::DEVELOPER

EBIIMCS and FIMM

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

AIMS

:: MORE INFORMATION

Citation:

Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A. A System for Information Management in BioMedical Studies–SIMBioMSBioinformatics2009 Oct 15;25(20):2768-9.