FAQ

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Contents

General

What is mx being used for?

What software is needed to run mx?

  • Mx can run on a wide range of platforms. See Installation.

Can you run mx locally and then sync your data to the server?

  • Not really. You could, however, run a copy in development mode locally, and prepare all your data there, then move that en-masse to production/the web.

Can I run mx without a web-based server?

  • Yes, the application can be run locally, though it hasn't been designed with this in mind or optimized (speed) for this usage. Keep in mind you won't be able to share the application over the network or internet, i.e. it could only be accessed at one machine.

How do I cite mx?

  • The short answer is however you see fit. mx was introduced at the 2006 TDWG meeting, however it looks a lot different now than it did then. Perhaps the simplest way is to cite it inline with the URL like "We used mx (code and documentation available at http://mx.phenomix.org) to {do stuff}."

Data model

Can I see the schema?

What do all the abbreviations in tables/fields mean?

Data entry/import

How do I load EndNote formatted reference into mx?

How do I load a Nexus file into mx?

  • See the "Phylo" tab and follow the directions here.

What mechanisms are available for entering data?

  • Data can be entered in a number of different ways
    • individually via forms
    • in batches via the web interface
    • in batches via the server side console (Rake tasks)
    • individually via the Rails console

Manually entering data one a time can be very annoying, what kind of data can I batch load into mx?

  • Matrix related
    • Nexus formatted matrices
    • Lucid's .xls formatted exports
    • Newick formatted trees
  • Specimen related
  • Nomeclature related
    • Single word epithets (children) of taxon names (e.g. species names for a genus or genera of a family)
  • Image related
    • Image files (via a Rake task/command line)
    • References to MorphBank images
  • Reference related
  • Sequence related
  • FASTA
  • Ontology related
    • OBO files (instantiates labels including synonymy, classes, relations, and references provided as xrefs)
    • Sensu tables ([label, definition, reference] combinations)

Can projects be merged?

  • Yes, data can be moved from one project to another, though not all synonymous data are merged at present. You'll need to use the console interface to do this. See the Proj#merge_to_project.

Data export/access

What formats can matrices be exported to?

  • OWL (CDAO), NeXML, Nexus, TNT, ASCII tables, and mx database tables

Is there an API?

  • Yes, an API is in early development, see App/API.

Production servers

What's the preferred production/development update path?

  • BACKUP DATA with 'rake mx:db:dump_data RAILS_ENV=production', a dump goes in app home/db/dumps. Update source (at present the latest source is on the relatively stable /edge/branch). Migrate the database with 'rake db:migrate RAILS_ENV=development' (you may want to test prior to or after this step with 'rake test'). Dump the data again (first step). Copy this copy to app home/db/dumps in your development environment. Load it with 'rake mx:db:restore_last' (note his dumps the current development, so if the reload fails you'll have to delete this dump as it will be more recent than your production copy). Develop. Repeat.

Clicking on a figure on a public site is giving me a 404, how do I fix this?

  • Choose edit for project settings and make the figure controller public by checking it.

Matrix based species descriptions

Can mx generate matrix based descriptions?

Yes. Mx has a very flexible content handling system which includes the functionality of using coded characters (sensu morphological phylogenetics) into species descriptions. This is similar functionality to that done in Delta, Lucid, or vSysLab, but with some modifications. See Matrix based descriptions.

Taxonomic names

Why can't I see taxonomic names in my project?

  • Visibility of names is dynamically set. Go to the Taxon names tab, then more options->visibility select the parent node you want visible. The taxon names will now be visible and available for use. Removing names from visibility does not delete them, nor invalidate records that reference those names. Visibility is used to focus your workflow, limiting the options in the dropdown, and the data you are reviewing.
  • After initial installation no names will be visible. To start adding real taxa after you create a project make the root taxon visible via the visibility view in the "Taxon names" tab. Then the root will available as the parent of the highest taxonomic level included in your taxa list.

Use the visibility list in the Taxon names tab to make root visible

I can't create a taxon name?

  • Permissions are set at a by taxon level, have your administrator update the permissions for the given user.

My taxon names are repeated in different colors, why?

  • See the application help here App/otu

OTUs

See 'What are all these colorful OTU names?'

  • See the application help here App/otu

Users

How do I add someone to my project?

  • Mx uses a FOAF system for creating new accounts. After you sign in navigate to http://yourserver.foo.com/account/signup. Signing up a new user also logs that person in, logout to return to your user. Select your project, click 'settings' and click the link to add a new user to a project.

General errors

I can't upload files, particularly pdfs, why?

  • Firefox has a known bug in which the MimeType can be corrupted. See [this page]. Close FF. Delete your mimeTypes.rdf file in your FF profile, reopen.

Production/server gotchas.

mx suddenly can't load pdfs or images.

rake db:migrate RAILS_ENV=production fails when a model is not found

  • This can occur when updates occur out of sync on in large groups. To resolve edit config/environments/production.rb and change the following line from true to false config.cache_classes = false, run the migrations, then set back to true.

This wiki

There used to be some pages on this wiki, now I can't find them?

  • Mx has been used/in development for over 5 years now, as such there are various "legacy" pages here on the wiki that may or may not have as much relevance as they do now. Legacy pages for references to these.
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