Frequently Asked Questions

A collection of FAQs, useful tips, and troubleshooting advice. Please, contact us to contribute your experiences!


General Questions


What is Megx.net? Megx.net is a portal that integrates environmental and genomic data for ecological analysis
What can I do with Megx.net? Megx offers three main functions:
  1. Mapserver Popup The Genes Mapserver can be used to view georeferenced genome, metagenome and rRNA sampling sites and selected physicochemical and biological parameters. You can view the behavior of these interpolated parameters in different time intervals via the Location link (right pointer above) or Interpolated Data link (left arrow above) in each sampling site pop-up window.
  2. Geographic-BLAST - can query the genome and metagenome databases we offer and view the distribution of your georeferenced hits. You can then use the Mapserver's functionality at any one of these locations.
  3. "Browse" functions - The "Browse" menu in the navigation bar offers additional functionality. EnvO-Lite (Revision 1.4), a subset of the Environmental Ontology project, was used to assign a large percentage of the microbial genome and metagenome collection a term describing the isolation source of the sequenced organism or community. Using our "Browse" page, you can easily view samples from similar isolation environments for comparison. A number of marine phages have been described in GCDML reports listing a variety of metadata. These can also be accessed via the Browse menu. You can use the mapserver's functionality for georeferenced entries by clicking on their coordinates displayed in the "Location" column.
Why do I need Megx.net? Environmental context is vital for all ecological analyses. Using Megx.net's environmental data extractors, microbial ecologists and marine scientists can better contextualize and compare extant biological data. Additionally, our manually curated meta-descriptors, such as EnvO-Lite annotations, offer further comparative perspectives and help expand the scope of your research.
What do I need to start using Megx.net? To fully access all components of Megx.net, you will need a web browser (we recommend the latest version of Firefox) with JavaScript and flash enabled...and a biological question.

How can I learn the basic concepts and

features of Megx.net?

Please view our flash video tutorial!
Can I use the data and analysis from Megx.net in my own research and publications? Of course, we are here to facilitate your research! If you find Megx.net useful, please cite:
Lombardot T, Kottmann R, Pfeffer H, Richter M, Teeling H, Quast C, Glöckner FO. Megx.net -- database resources for marine ecological genomics. Nucleic Acids Res. 2006 Jan 1;34 (Database issue): D390-393. [Pubmed Abstract] [Free full text]

General Questions


What does 'NA' mean throughout the site? We use 'NA' as a shorthand for 'not available'. This means the underlying data is missing. We have an undergoing curation effort, which aims to enrich the data content and quality. If you would like to contribute, please, do not hesitate to contact us.

Genes Mapserver


Why doesn't the Genes Mapserver map load? Make sure JavaScript is enabled in your browser.
How do I zoom into a region of the map? You can either use the navigation bar on the right of the screen, or hold Shift on your keyboard and, using the cursor, drag a selection rectangle around the region you wish to view.
How are the physicochemical layers rendered? Values in our database are binned into intervals displayed in the legend of each physicochemical layer and assigned a colour. Please note, overlay shading should be used for guidance purposes only as some intervals are not assigned regularly separated colour values. Please contact us if you require information on the exact RGB values used.

Geographic-BLAST


Which databases can I search against with the Geographic-BLAST? For details on the available Geographic-BLAST databases, please, check our content page.
Why are there fewer points on the Geographic-BLAST map than there are georeferenced hits in the results table? After a certain threshold, BLAST hits in the same location are represented by crosses of different colours (see the legend below the map). Zoom into the area or click on the cross to view the hits at that site.
Why doesn't the Geographic-BLAST map load above the BLAST results table? Check that JavaScript is enabled in your browser.

GIS Tools


What is the big deal about these GIS Tools? This is one of Megx.net's most unique features!
Upon providing latitude/longitude coordinates for any marine location over a specified time interval, a user can request physicochemical parameters interpolated from primary data of the World Ocean Atlas (WOA05) or World Ocean Database (WOD05).
What is the "Environmental Stability" layer? This layer reports the per annum standard deviation (SD) of a selected parameter's monthly values at a user-specified depth.

EnvO-Lite


What is EnvO-Lite and how was it applied

here?

Please see the EnvO homepage and our Annotation Overview for details
How can I use the EnvO-lite annotation? Our "Browse" page allows you to view the annotation. Clicking on a habitat or environment in the tag cloud will populate the table below it with organisms thus annotated. This grouping may be the starting point of many comparative analyses and perspectives to complement your research!
Are more annotated genome projects available? Yes! Please contact us and we'll be happy to provide you with the latest and most complete annotation we have.
Can I retrieve further environmental information from the "Browse" page? If an entry is georeferenced and its geographic coordinates are displayed in the "Location" column, simply clicking on them will allow you to use our Genes Mapserver to retrieve a number of ecological parameters characterising its sampling site.
What if an entry is wrongly annotated? If you find an error in the annotation, please let us know and we'll attempt to correct it. In such cases, we would greatly appreciate directions to any supporting literature or other documentation with sample isolation information.

MegDB Database Content and Web Services


How can I get a custom-filtered list of genomes (ie: what are all the complete, georeferenced marine genomes?)? Just ask us! Our underlying database, MegDB, contains much more than is accessible via the web, which provides only a limited view on the data and by no means reflects the full structure and content of the database. As such, we would still like to make the most use of our service, so let's talk and do science.