A collection of FAQs, useful tips, and troubleshooting advice. Please, contact us to contribute your experiences!
|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:
|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.|
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]
|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.|
|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.|
|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.|
|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.|
What is EnvO-Lite and how was it applied
|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.|
|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.|
now extensionurl = //gms-dev.megx.net/map