Pan African Bioinformatics Network for H3Africa

H3ABioNet provides access to experts from a variety of domains to help answer any bioinformatics related questions and provide support to various H3Africa and non H3Africa projects that might be struggling with the analysis and planning of their experiments. The H3ABioNet helpdesk system accepts requests from the H3ABioNet web portal registered and non-registered users and can be accessed from here.

Definition of H3ABioNet helpdesk terms used

  • User:  An individual who submits a query for assistance to the H3ABioNet helpdesk.
  • Reps: An H3ABioNet helpdesk expert that is registered with the H3ABioNet web portal and responds to any submitted helpdesk query by a user and edits the tickets created by users.
  • Admins: An H3ABioNet helpdesk expert who is registered with the H3ABioNet web portal and assigns tickets to the Reps and is able to respond and edit tickets, re-open closed tickets and access reports.
  • Department: A department defines a common group or function in an organization for which a series of problems may be entered into the H3ABioNet helpdesk system. In the context of the H3ABioNet helpdesk system, the different departments are mapped to the various H3Africa research projects. There is also the term "None" mapped to the departments within H3ABioNet for users who wish to submit a H3ABioNet helpdesk query and are not part of any of the H3Africa projects. If an H3ABioNet helpdesk ticket is submitted via email (see section "Submitting a Query to the H3ABioNet helpdesk") and not the dashboard interface, the query is automatically assigned to the department of None
  • Categories: H3ABioNet has various domain knowledge experts (Reps) that range from bioinformaticians to administrative consultants that are internally grouped to a specific domain and form a pool of Reps for who that submitted query will be assigned to. For a listing of categories and number of experts present in each category, please visit here.
  • Query: A submitted question / request for assistance by a User to the H3BioNet helpdesk
  • Ticket: The submitted query is assigned a tracking number for which all communication regarding the submitted query is mapped to i.e. a ticket number. This enables the Users, Reps and Admins to easily determine the status of each query, time taken to resolve the query and easily sort / filter any communication for that submitted query. Sometimes the term query and ticket are used interchangeably.

Schematic overview of H3ABioNet helpdesk ticket submission process

Process flow of a user submitted query to the H3ABioNet helpdesk.

A User submits a H3ABioNet helpdesk query via the submission interface which is assigned to an Admin user who will check what Category the query belongs to, who is available to answer the query and assign the query to that Rep. The Rep will answer the query or request the User to submit more information in terms of providing context of the problem if necessary. The H3ABioNet helpdesk Rep and User will work together until the query has been resolved.

Submitting a query to the H3ABioNet helpdesk

Queries can by users can currently be submitted to the H3ABioNet helpdesk using 3 different methods:

  1. Directly from the H3ABioNet helpdesk web portal. This option is available to H3ABioNet registered and non registered users. The difference between a registered user and a non-registered user is the former can log into the H3ABioNet website and view the history of all the tickets that they have submitted and their status. For the latter, the status of each submitted ticket can only be queried individually via a simple interface.

    Screen shot of the H3ABioNet helpdesk query submission interface used to submit a question to H3ABioNet by a user.

  2. An H3ABioNet helpdesk Admin can create ticket on behalf of a User upon a request for any assistance and provide the ticket number to the User for subsequent communication

  3. Tickets can automatically be created by sending an email to This email address is being protected from spambots. You need JavaScript enabled to view it. (although this is not recommended).

The user selects the Category their query falls within, chooses the Department (H3Africa project they are part of or "None" if they are not part of an H3Africa project), enters their email address and provides a title in the form of a question. The user then inputs the details of the query they have into the description box and clicks on "Submit". The user will receive an email acknowledging their submission which will contain an ID number (ticket number used for tracking by the H3ABioNet helpdesk system).

Additional information can be added to a ticket by sending an email directly to This email address is being protected from spambots. You need JavaScript enabled to view it.  and quoting [psn:X] in the subject line where X is equal to the ticket number.

After submitting a query to the H3ABioNet helpdesk

The H3ABioNet helpdesk Admin will receive the query and based on the category entered by the user and will assign the query / ticket to an H3ABioNet helpdesk expert (a Rep). The Rep or Admin will also assign a priority to the submitted ticket which could be:

  • LOW
  • HIGH

The Rep will then endeavour to answer the query submitted by the user via the H3ABioNet helpdesk interface. While the H3ABioNet helpdesk Rep is working on the user submitted query, the ticket itself has a status which can be modified by a Rep or Admin. The various options for the status of an H3ABioNet helpdesk ticket are:

  • NEW
  • OPEN
  • HOLD

These statuses will change during the life cycle of the submitted query until it has been fully answered and the ticket associated to the query can be closed.

H3ABioNet helpdesk interface for Reps. Reps can set the status and priority of a submitted user query and report on the time spent working on that query.

Tracking of communication for a H3ABioNet helpdesk user submitted query

There will usually be some communication between the Rep and user on the query that was submitted before a final solution is reached. The H3ABioNet helpdesk system enables the tracking of various threads of communication revolving around that query via the ID / ticket number via a convenient web based interface. An email is also sent to the Rep and the user whenever an update to the submitted query is made such as when a Rep or user replies on a ticket (in the Enter Additional Notes field) so both the user and Rep can attend to the update.

An example of interaction and additional notes taken between a user and Rep.

Closing of user submitted query / ticket

Once a final solution for the problem has been reached to everyones' satisfaction, the Rep can enter a summary of this solution within the "Solution" box of their interface and close the ticket. The information / final solution provided will be entered into the Knowledge base portion of the H3ABioNet helpdesk system upon the Rep's and Admin's discretion for use in generating FAQs and also providing solutions to any similar queries that might be submitted in the future by another user. The Knowledgebase is a searchable database of user submitted queries to which a solution has been achieved and can only be queried by Reps and Admins.

Adding attachments to a H3ABioNet helpdesk query

Currently attachments cannot not be sent to the H3ABioNet helpdesk when a user creates a ticket. A user or admin would first need to create a ticket and then only can a user submit an attachment to the H3ABioNet helpdesk by sending an attachments can be send to  This email address is being protected from spambots. You need JavaScript enabled to view it.  and quoting [psn:X] in the subject line.

Additional resources and discussion forums related to Bioinformatics

  • SEQanswers: a discussion forum and information source for next generation sequencing
  • SBS: Swedish Bioinformatics Support
  • BioStar: a StackExchange based question/answer site for bioinformatics
  • Rosalind: Rosalind is a platform for learning bioinformatics through problem solving
  • Stack exchange: Provides access to different forums for computer code related problems