epiPATH is an open source bioinformatics platform to store and analyze evolutionary, population and epidemiological data from infectious diseases. It focuses mainly on pathogens and their sequences that are obtained in a laboratory. This software is designed to aid users in daily work with the large amount of data generated in sequencing projects as well as clinical and epidemiological data. It constitutes a kind of Laboratory Information Management System (LIMS) that is oriented towards the analysis of both types of data (clinical and molecular) at the same time.
As open source software, epiPATH source code is freely distributable and available to the general public under the GNU General Public License, and therefore it could be downloaded, used and modified, but the access to our platform is only possible for the personal of our institution. Security issues have been very relevant in developing this platform and are also available to those users that want to implement epiPATH in their own laboratories. Data confidentiality must be maintained due to ethical and scientific reasons.
The software architecture consists of (1) a Web-based User Interface written in XHTML, CSS, JavaScript and PHP, (2) a MySQL database, which contains all clinical, epidemiologic and molecular data divided in 12 conceptual modules and (3) different analysis and data management tools.
The web interface gives access to data and its management. The tools implemented are those to insert, update, search and delete information in the epiPATH database server and several more to perform analysis with data stored or external data. Most of the analysis tools implemented in epiPATH platform have been developed by different people outside our laboratory. We have included them in our platform following their public or academic licenses. For more information about using these tools, please visit their homepages or see instructions at each tool section in the web interface. Tools implemented include Sequence Database Similarity Search (Remote NCBI Blast, Local epiPATH Blast and File Blast), EMBOSS (Tranalign and Transeq), Multiple Sequence Alignment (MUSCLE, T-Coffee, MAFFT and ProbCons), EPP-tools (Divergence, Neutrality, Polymorphism and Synonymous), Libsequence (compute), Statistics (coalescence) and Utils (RevTrans).
To access all this tools and data you must have an authorization with username and password. If you have epiPATH implemented in your institution and you want to have access, please contact with your System Administrator.
December 2008 :: New bug detected at fixed bug list.
September 2008 :: epiPATH platform version 2 is released.
December 2008 :: New bug detected at fixed bug list.
September 2008 :: epiPATH platform version 2 is released.
July 2008 :: We are upgrading epiPATH platform in our local server. Distribution files of epiPATH platform version 2 and new documentation would be available soon.
January 2008 :: We have improved our local server in order to achieve more speed in all processes.
September 2007 :: We have added epiPATH project in sourceforge.net.
April 2007 :: epiPATH has been published. See Citation section.
March 2007 :: A new version of epiPATH is being tested locally. It would be released very soon.
January 2007 :: We are working in a new epiPATH web interface and adding analysis tools.
24 October 2006 :: epiPATH version 1.1 released [fixed bugs]
This software has been created and developed by Alicia Amadoz Navarro and Fernando González-Candelas in the Evolutionary Genetics Group at the Cavanilles Institute for Biodiversity and Evolutionary Biology of the University of Valencia.
We hope many researches to download and use epiPATH, and wish to receive feedback about their experience in order to improve this bioinformatics platform.
epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.
Amadoz, A. and Gonzalez-Candelas, F.
BMC Infectious Diseases 2007, 7:32.
These images are from epiPATH platform version 2
These images correspond to the epiPATH versions 1 and 1.1
Last modified ::: 6 Dec 2008
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