User guide

Mobyle allows to run bioanalyses through a web interface without installing anything locally. The Mobyle public portals provides an access to more than 200 bioinformatics programs of Sequence Analysis, Phylogeny, Structural bioinformatics or Genomics.

Key features of Mobyle

Programs menu

Programs available through Mobyle Portal are sorted by categories displayed as a tree in the left menu. A program can be in several categories.
Using the search functionality, you can retrieve a program or programs related to your search. For example, you will retrieve all programs where temperature is asked searching "temperature".
To best way to start is to use the search functionality or to have a look at a given category which fit with your wishes to know what are the available programs.

Your own account

If you want, you can create your own session. The main advantages are that once you are registered you can access your last submitted jobs (they remain 10 days on the server) and bookmark data of interest to re-use it later, through respectively Jobs and Data Bookmarks sections in Mobyle left menu.
If you are not interested in, it is also possible to use mobyle without having your own account. In this case, Mobyle will anyway ask your email to be able to send you notifications or results for long jobs in particular.

Here is the procedure to register:
  1. Click on the sign-in link located on the top right of the page, then click on register.
  2. Enter your e-mail, and pick a password (this password is specific to the portal).
  3. Once submitted, you will receive an e-mail requesting your confirmation for this registration.
  4. You can then save your data, and access them from anywhere.

Further analysis

There is a type compatibility mechanisms between results and potential program inputs that allows you to interactively pipe tasks. You will visualize this functionality in the result page of your jobs with a list of compatible programs with your output and a Further analysis button.

Watch How to run a job

This is a short video to illustrate basic use of Mobyle.

Where to find documentation in Mobyle

Tutorials section

In the Mobyle left menu, you can find a Tutorial section containing some documentation about:
  • how to use Mobyle (example and indications to help you to handle the portal)
  • details to create your own account if you want
  • the Sequence and Alignment formats recognized by Mobyle.

Programs Documentation

For each programs available in Mobyle portals, all the available documentation is provided through 3 ways:
  • red question-mark(s): they are present at parameter level and clicking on the question mark, you will find information about the corresponding parameter such as example data or accepted format.
  • help pages: link(s) displayed at the bottom of the form to the help documentation written by the program author(s).
  • references: paper(s) related to the program.

As programs are all free, documentation provided by the author(s) is sometimes not very abundant.

Ask for help

In your results page, there is a Ask for help button that send an help request to the Mobyle portal administrator(s). We recommend to read first all available program documentation before asking for help because in most of the cases, the answer to your question is on the documentation!
This must be used when the program returns an error that you can not understand or if you detect a problem in the form for instance.
(The questions of the following section were sent to us through Ask for help button.)

Frequently asked questions

  • Why do I have this on my job results:
    error message: Your job finished with an unusual status code ( 1 ), check your results carefully 

--> A software finished with a status code. If this software follows good programming practices the status code worth 0 when this one is finished correctly and with another value when it encountered a problem. In this case usually a message is associated to explain the problem. However lot of bioinformatics software doesn't followed this good programming practice and finished with a status code different from 0 even if the program doesn't encounter any problem. Thus if you have such message either there was a problem during the program execution or this software have a poor programming practice. Check carefully all the results to find any error message.

  • When I want to submit a form, I have the error message:
    parameter name : Cannot detect the alignment format. The supported alignment formats are: ['NEXUS', 'STOCKHOLM', 'CLUSTAL', 'FASTA', 'PHYLIPS', 'PHYLIPI', 'MSF']

--> The data you provide for the parameter doesn't match with any alignment format managed by Mobyle. Please check your data and the examples of different alignment formats managed by Mobyle in Tutorials section.

  • When I want to submit a form, I have the error message:
    parameter name : Cannot detect the sequence format. The supported sequence formats are: ['IG', 'GENBANK', 'NBRF','EMBL', 'GCG', 'FASTA', 'RAW', 'PIR', 'SWISSPROT', 'GDE']

-->The data you provide for the parameter doesn't match with any sequences format managed by Mobyle. Please check your data and the examples of different sequence formats managed by Mobyle in Tutorials section.

Last update: Mis à jour il y a presque 9 ans