End of H3ABioNet grant Notice

: Communications; 18 February 2025; Hits: 661

The H3ABioNet grant has come to an end after 12 years of funding. Therefore, we will not be updating or adding any new information to the website. However, you can continue to access or find new locations for H3ABioNet generated tools, training, standards and resources on this website. NB: the H3ABioNet helpdesk will remain active and is now accessible as part of the AfriGen-D helpdesk (https://helpdesk.afrigen-d.org./helpdesk/).

Some of the H3ABioNet projects have continued under new funded grants, you can find links to the new project websites below. Where applicable, links have been provided from H3ABioNet to their new locations:

eLwazi Open Data Science Platform (ODSP):

The eLwazi consortium is a collaboration across multiple institutions aiming to develop an Open Data Science Platform funded through the DSI-Africa Initiative. eLwazi is adapted from ulwazi, a Nguni word for “knowledge” or “information”, and olwazi, meaning big rock in Luganda. The aim of eLwazi is to provide an African Open Data Science Platform and associated resources to support the Harnessing Data Science for Health Discovery and Innovation in Africa (DS-I Africa) consortium and beyond. The vision of the eLwazi is to provide users with a flexible environment for 1) depositing, sharing, and accessing data, 2) selecting data-specific tools and methods, 3) Deploying tools and workflows suited to the African context, to facilitate novel discoveries for health.

eLwazi Open Data Science Platform (ODSP) website: https://elwazi.org/

African Genomics Data Hub (AfriGen-D):

African Genomics Data Hub (AfriGen-D) website: coming soon!

African Bioinformatics Institute (ABI):

African Bioinformatics Institute (ABI) website: coming soon!

events current , featured

WIDS AFRICA CONFERENCE

: Communications; 15 February 2021; Hits: 17407

Conference Overview/description:

WiDS Africa is an independent event that is organized by H3ABioNet based WiDS Ambassadors in collaboration with other African based WiDS Ambassadors from MARI and dlab as part of the annual WiDS Worldwide conference organized by Stanford University and an estimated 150+ locations worldwide, which features outstanding women doing outstanding work in the field of data science. All genders are invited to attend all WiDS Worldwide conference events. We are hosting a WiDS Africa regional event to engage our community of diverse women in Data Science. We will watch the WiDS Stanford Livestream as well as feature Africa specific lightning talks, panel discussions, Keynote speech, and end with a networking event.

NB: Registration and Attendance of Conference is FREE

<<Register to be a participant in WiDS Africa by clicking here>>

Registrations close 03 March 2021

Intended Audience:

This conference is aimed at; Women in Data Science, Early Career Researchers, Fellows, MSc, PhD trainees, postdocs. Academics, Government and Industry officials. Anyone interested in data science. All genders are welcome.

Conference objectives/outcomes:

• Listen to and engage with a diverse group of women in data science through panels and talks

• Networking

• Advocacy

• Promote Data Science in Africa especially for women

Prerequisites:

None. Just be interested in Data Science and promoting gender diversity in the field.

Dates for the Conference:

Monday 8 March 2021

Conference registration opens:

04/02/2021

Classroom registration closes:

03/03/2021

Notification date:

Immediately after registration

Participant registration:

Registrations are now open, please register here. Registration close 3 March 2021 at 11:59 pm CAT.

Workshop organisers:

African based WIDS Ambassadors — H3ABionet: Paballo Chauke, Nicky Mulder, Caleb Kibet. dlab: Mahadia Tunga. MARI: Jacki O'Neill. BMGF: Amel Ghouila

Workshop Sponsors:

WiDS Stanford University

WIDS

Keywords:

Data Science, Women in Science, International Women's Day

Skill level of training:

Beginner to Advanced

Language:

English

Credential awarded:

N/A

Type of meeting:

Virtual

Conference Programme:

Monday 8 March 2021: African WIDS Regional Programme

Time (CAT)	Session Title	Speaker/s	Facilitator/ Moderator
14 :00 – 14 :10	Welcome and Introductions	Nicky Mulder and Mahadia Tunga	Mahadia Tunga
14 :10 – 14 :30	Opening Talk	Amel Ghouila (BMGF)	Mahadia Tunga
14 :30– 15 :00	Panel Discussion on Impacts of the Pandemic on women in data science	Speakers: Chenai Chair (Mozilla) Rahab Wangari(Hepta Analytics) Ruthbetha Kateule(UD) Dominique Anderson (SANBI)	Verena Ras
15 :00- 15 :05	*Break/breather*		Verena Ras
15 :05-15 :12	Graduating during a pandemic	Samar Elsheikh	Mahadia Tunga
15 :12- 15 :30	*Launching your career as a data science consultant* 2 speakers 7 mins each (14 + 3min Q&A)	Hellen Maziku (UD) Catherine Cress	Mahadia Tunga
15 :30- 16 :00	KEYNOTE PRESENTATION	Mamokgethi Phakeng (UCT VC)	Mahadia Tunga
16:00- 16 :10	*Young girls in DS- passing the baton and being black/POC in DS*	Jenea Adams (BWCB) Winfred Gatua (PU)	Amel Ghouila
16 :10-16 :15	Closing and Thank you remarks		Nicky Mulder
16 :15-17 :00	Networking session	Everyone	Olawumi, Verena, Amel, Mahadia and Jacki

Speakers Country of Origin:

South Africa
Tanzania
Tunisia
Rwanda
Kenya
USA

Logos of organizers/ collaborators:

current

H3ABioNet Helpdesk

: Communications; 20 February 2018; Hits: 7930

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:

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.
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
Tickets can automatically be created by sending an email to (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 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:

VERY LOW
LOW
NORMAL
ELEVATED
HIGH
VERY 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
RECEIVED
OPEN
IN PROGRESS
ESCALATED
HOLD
WAITING
TESTING
CLOSED

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 anattachments can be send to 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

Genome Detective Coronavirus Typing Tool

: Communications; 24 April 2020; Hits: 10568

Genome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS) related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole-genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs, and vaccines to stop the COVID-19 disease. Read more.

Source: Bioinformatics, 2020.

covid-19

FAQ

: Helpdesk; 20 February 2018; Hits: 17716

1. Can I submit a ticket even if I am not part of the H3Africa consortium?

Yes, anyone can submit a query. This service is open to all scientists in Africa on the project name please choose “Other”.

2. Why do I need to fill in all the information requested when I submit a ticket?

We need this data for reporting purposes. It will not be used against you in anyway.

3. Can I ask one of the HelpDesk members to perform an analysis for me?

We would prefer to keep this as an informational HelpDesk. We would suggest that you set up a collaboration agreement between you and the HelpDesk rep you are working should you need some analysis done for you.

4. Can I submit an attachment as part of the ticket?

A user or admin would first need to create a ticket and then only can a user submit an attachment via email. Send attachments to and quote your ticket number in the subject line.