Bioinformatics software is an emerging market due to constant decrease in genome sequencing costs. High quality software to manage, store and analyze the Petabytes of biological data produced in the public and private sector is greatly needed. The Macedonian software company, InterWorks, collaborates with the Microbial Genomics Group from the Max Planck Institute for Marine Microbiology to further develop the internet platform for Microbial Ecological Genomics, megx.net. The goal is to enable megx.net's social networking technologies to provide a unique integrated platform for quality driven ecological analysis of high-throughput genomic data from the world oceans.

An employee of InterWorks will work on a scientific Master's Thesis project with this aim, under the supervision of Prof. Dr. Markoski from the University “St. Kliment Ohridski” Bitola together with Prof. Dr. Frank Oliver Glöckner and Renzo Kottmann, PhD, from the Max Planck Institute for Marine Microbiology. InterWorks sponsors this scientific endeavor by providing essential resources and expertise in software development.

This trilateral collaboration explores new pathways between academia and industry by pooling expertise and resources in a unique way: the software company, InterWorks, transfers excellent software engineering practice to academia, the Microbial Genomics Group introduces bioinformatic expertise, and Bitola University further complements this triangle with environmental informatics expertise. Through this innovative public and private sector partnership with graduate education in Macedonia, the collaboration intends to seed long-term collaboration, benefiting all by combining expertise in high quality software production with specific bioinformatic knowledge of biological data management and analysis.

Our abstract

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.

Click on Abstract, Full Text, PDF

The full citation for our article is:

Megx.net: integrated database resource for marine ecological genomics Renzo Kottmann; Ivalyo Kostadinov; Melissa Beth Duhaime; Pier Luigi Buttigieg; Pelin Yilmaz; Wolfgang Hankeln; Jost Waldmann; Frank Oliver Glockner Nucleic Acids Research 2009; doi: 10.1093/nar/gkp918

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We have launched release 6 of megx.net. New datasets for the Genes Mapserver and Geographic-BLAST are now available, including:

• marine metagenomes from the Global Ocean Sampling (GOS) Expedition
• marine phage genomes
• diversity data from the SILVA RNA database

More details on the data can be found on our content page.

To improve the usability and understanding of our resources we have added:

• megx.net video tutorial
• Web Map Service tutorial
• Frequently Asked Questions (FAQ) page

Sampling site detail pages now include detailed information about the corresponding samples, including in situ data where available. You can start browsing the list of sampling sites.

Please contact us if you encounter problems or to give us your feedback.

We have launched release 6 of megx.net. New datasets for the Genes Mapserver and Geographic-BLAST are now available, including:

• marine metagenomes from the Global Ocean Sampling (GOS) Expedition
• marine phage genomes
• diversity data from the SILVA RNA database

More details on the data can be found on our content page.

To improve the usability and understanding of our resources we have added:

• megx.net video tutorial
• Web Map Service tutorial
• Frequently Asked Questions (FAQ) page

Sampling site detail pages now include detailed information about the corresponding samples, including in situ data where available. You can start browsing the list of sampling sites.

Please contact us if you encounter problems or to give us your feedback.

The latest version (release 4) of Megx.net is now available! Check out the new features:

• Search for proteins of interest in a geographic context using the new Geographic-BLAST, implementing the new mapserver.
• Organisms sequenced through the Moore Microbial Genome Sequencing Project are now manually georeferenced, an essential component for full functionality of Megx.net features.
• Find a Sampling sites details page for all sample points on the map. Simply click on any point and follow the link to learn about all samples taken at that location, as well as on-site environmental parameters.
• Especially unique to Megx.net, learn about the long-term environmental stability of each sample site. On the Sampling sites details page, you will find annual and monthly averages of on-site parameters from the World Ocean Database.

Please contact us if you encounter problems or to give us your feedback.

A new megx.net release is available. Based on user feedback, a couple of dozen bugfixes and enhancements were made. Highlights among others are:

• The menu bar should now also work in a nice way for Internet Explorer >5 (We have only limited access to Internet Explorer for testing).
• The Genomes Browser includes Genome Project Identifiers with links to ENTREZ Genome Project pages.

Please, contact us if you have encounter problems or give us your feedback

Today the new megx.net portal was launched

It includes not only a new face-lift, but also many new features.

MetaLook, a 3D visualisation software for marine ecological genomics, is now available at: http://www.megx.net/metalook. It is also published under an Open Access licenses at http://www.biomedcentral.com/1471-2105/8/406/