# Open Science Seminar at EANBiT Virtual Training

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The East African Network for Bioinformatics training (EANBiT), seeks to upskill students in Bioinformatics using the model: coursework, 5-week residential training and finally research project placement at partner institutions. EANBiT works with universities in Kenya, Uganda and Tanzania, to offer MSc in Bioinformatics. It supports curriculum development, offers MSc fellowships to students, and support placement for research. The residential training (gone online this year), has four tracks: technical, Soft skills, Seminars, and Mini projects. The seminars involve talks from leaders in various areas of genomics, including open science.

For open science, in collaboration with H3ABioNet, we seek to expose the students to:

* Open Science principles, and how they apply to our fellows' research, now and in the future
* Practicing and promoting reproducible and collaborative research - _The Turing Way_
* Data and Education in Low-income settings: David Selassie
* Leveraging and building a community in science and research - Open Life Science mentoring program
* How to get involved in local communities - Galaxy Africa

**When:** 29th July, 2020

**Time:** 1600-1800 GMT+3

**How:**
* Four presentations of **15 minutes** each
* A **20 minutes** breakout session
* A **40 minutes** panel discussion and Q&A

Where:

Website: http://eanbit.icipe.org/

Repo: https://github.com/eanbit-rt

## Kindly type in your name, affiliation, Twitter handle

Caleb Kibet / ICIPE / @calkibet
Eneza Yoel / Pwani University / @ene_yoel
Ritah Nabunje / Makerere University / @RitahNabunje
Michael Landi / ICIPE / @CofiaLandy
Yo Yehudi / Wellcome Trust & Open Life Science / @yoyehudi + @openlifesci :)
Martha Luka / ICIPE & KEMRI-Wellcome Trust Research Programme / @martha_mawia
Wasswa Razack/Makerere University/ @wrazack
Ibra Lujumba / Makerere University
Stella Esther Nabirye / Makerere University / @StellaNabirye1
Margaret Wanjiku / ICIPE & BecA_ILRI Hub / @meg_wanjiku
Joseph Mulama / Pwani University & ICIPE / @MulamaJoe
Festus Nyasimi / ICIPE / @Festus_nyasimi
Olga Nsangi Tendo / Makerere University / @KibayaO
Paul Talent/Makerere University/@talzpaul
Omara Isaac Emmanuel / Makerere University / @IsaacEmmanuel89
Ivan Sserwadda/ Pwani University / @ivangunz23
Verena Ras / H3ABioNet / @RasVerena
Evans Mudibo/ Pwani University/ @mudibo_evans
Winfred Gatua / Pwani University / @gatuaprof
Mthande Sibonakaliso M/ Makerere University
Davis Kiberu / Makerere University
David Selassie Opoku / Growing Gold Farms / @sdopoku
Jane Njeri / Pwani University / @NjeriAquila
Tumuhimbise Peninah / Makerere University / @T1_penny
Ruth Nanjala / Pwani University / @Ruthnanje
Dlamini Senamile F/Makerere University/@sena_dlamini
Malvika Sharan / [The Turing Way](https://github.com/alan-turing-institute/the-turing-way) / @malvikasharan
Abdoulaye Diawara/African Centre of Excellence in Bioinformatics, University of Science, Technology and Technology in Bamako (USTTB)Mali.
Akurut Eva / Makererere_University/@EvaAkuru
Peter Muchina / Pwani University /@kimanimuchina1
Shahiid Kiyaga / Makerere University/ @Ashaky
Lwasampijja Baker/ Makerere University

### Add questions to the panel here
- Is licensing of your research work a limitation to open science?
- Do you think having free publication, say as it is in Wellcome Open Research can enhance open science in LMICs?

## Panel

### Selassie David Opoku

1. Contextual Open Science. How can Africa ease into the adoption of open science principles in a way that works, beneficial, and in tune with our challenges?
2. What is the cost of open science? Are we willing and able to bear the cost?
3. Speak on openness and collaboration in different spaces: Data Science, Computational Biology, Low-tech training.
4. Any other aspect of interest to you

### Malvika Sharan

- Slides available online: https://zenodo.org/record/3968440

1. The Turing Way: https://github.com/alan-turing-institute/the-turing-way
- Join the Slack: join.slack.com/t/theturingway/shared_invite/zt-fn608gvb-h_ZSpoA29cCdUwR~TIqpBw
3. Collaborative and reproducible research
4. What it means to be a community builder, and why community building is essential
5. Any other topics of interest to you

### Yo Yehudi/Bérénice Batut
1. Introduce open science [slides](https://docs.google.com/presentation/d/1JrWBT9mc9yGldy-dj0aohjkp58ZlY0z5LlNk724ROTc/edit?usp=sharing)
2. Audience question: What does open science mean to you?
- Sharing
- Open Source, Open Data & Communities of Practice
- Working collaboratively and making data easily accessible
- Interoperability
- Accessibility
- Easy access and reusability
- Benchmarking
- Sustainability and reproduciblity
- Easy for the next person to
- Border less and free access to data generated responsibly for the use of others for a common purpose. Is it ethical to share data that is generated unethically? What lesson can we learn if not shared?
- accessible science
- free access
- Reproducible, accessible, shareable and openly accessible even to less privileged research communities.
- Let the world know what you're doing

3. Audience question: Are there scenarios where science shouldn't be open?
- Share data that can benefit humanity responsibly. It is not about not to share the genotype data but how to share genotype data such that with no risk.
- Personal data
- Private/individual data: genomics for example
- Indigenous land information
- Privately sponsored research work esp in within an African setting
- Medical data that requires participant consent
- Where benefit sharing is not assured (e.g. patenting of MERS genome in Europe, "helicopter science" where Northern researchers study Southern subjects with no benefit sharing)
-
- Mobile data (phones)
- If the openess violates rights!
-
3. Open Life Science in the context of open leadership
4. Who can get involved in OLS, and how?
5. Any other topics of interest to you

### Galaxy Africa (Peter Van Heusden)
(slides: https://docs.google.com/presentation/d/1XAIPxJgrDCekvFnx-fCkdC7t6e1PR1J_UHtjk2xFF1k)
1. Introduce Galaxy and Galaxy Africa community
1. How can we leverage Galaxy for Collaborative and reproducible research
1. How to join and engage in Galaxy Africa community

## Discussion questions during the breakouts

The [Open to Discussion](https://github.com/baricks/opentodiscussion) cards or questions can be used here. We will have 5 groups, each picking a question or two from the categories. There are different topic areas for discussion on the cards. Here are the different topic areas:
- **Group 1:** [Open Collaboration](https://github.com/baricks/opentodiscussion/blob/master/OpenCollaboration)—Malvika
1. If I share my work with other researchers, they might try to claim my work as their own.
1. I don’t want to invest a lot of time helping others who might end up taking all the credit.
1. If I choose to collaborate with other researchers on a project, I don’t understand who will be the first author of the publication.
1. Contributing to collaborative projects has helped improve my productivity.

Notes:
- Eric:
- Often new researchers may feel the fear of sharing and losing
- Teaching is not practiced everywhere
- Trust building takes time
- Stella:
- People who are junior in the group end up having to work a lot and not get fair credit, which can be demoralising.
- developing online on GitHub can create transparent way to get credits
- Ivan:
- Have been collaboratively working with others.
- It has been really useful for learning new skills and make my work better
- In some instances, it is hard to work together and synchronise what we are doing
- https://openlifesci.org/ols-2#resources
- https://github.com/open-life-science/open-life-science.github.io/blob/master/CONTRIBUTING.md
- How to hold people responsible for their tasks?
- Define bigger goals, and further divide them in smaller subtasks (Agile development)
-
- We hold coworking calls to create accountability for members who want to work with us
- Link to coworking: https://deploy-preview-1257--the-turing-way.netlify.app/community-handbook/coworking.html

- **Group 2:** [Open Data](https://github.com/baricks/opentodiscussion/blob/master/OpenData)—Yo
1. I’m worried that other researchers will make use of my data and get better results.
3. I’m fine with my personal data being used for important or groundbreaking scientific research as long as it’s anonymized.
4. I’m not sure how to begin making my data open. The process seems complicated.
5. There is insufficient training in documenting the process of making data open.
6. Decisions to make data open should be a responsibility of the institution, not of the individual researcher.
7. My collaborators don’t seem to care about protecting personal data.
8. I want to work with open data but it's easy to identify individuals in pseudonymized data.
9. My research is so specific. Nobody else would be interested in or be able to understand my data.
- **Group 3:** [Open Education](https://github.com/baricks/opentodiscussion/blob/master/OpenEducation)—David
Notes:
What is Open Data Education?
- Free access
- Share access
1. I spent hours working on my slides and my syllabus, so I don’t see why I should share them
- Opportunity to get feedback from others
1. I want to be credited for all the work I put into designing the curriculum, even if I share it with other educators.
1. I’ve been told that commercial educational materials are more reliable but I’m not sure.
- Commericialising gets the best people to work on materials because they are being paid. However making it open will allow more diversity and contributions which will improve the resource.
- It really depends on the scenario or situation.
- Examples of operating systems of Microsoft or MacOS being commercial whereas Linux being open-source. Is one better than the other?
1. There is too much overlapping material and curriculum already out there in education.
- **Group 4:** [Open Source](https://github.com/baricks/opentodiscussion/blob/master/OpenSource)—Peter
1. Open source means that every part of my code should be shared.
1. I’m nervous that others will find faults with my research results if my code is open.
2. "Imposter syndrome" is sometimes a barrier.
3. I spent hours debugging and troubleshooting my code, so I’m not going to give it away for free.
4. I use open source software but to be honest I don’t know how to contribute.
5. Many people are focussed on their research and contribution takes time that they do not have.
6. My institution pays to purchase licenses so I don’t need to use open source projects.
6. Many people use software because it is freely available. It is not so much open or closed that makes the difference as cost.
7. Sometimes the software is installed by the IT Department but many people install software themselves.
7. In research projects, we should set aside part of the budget to spend on making the results openly available.

- **Group 5:** [Open Access](https://github.com/baricks/opentodiscussion/blob/master/OpenAccess)—Caleb
1. My supervisor doesn’t want me to submit my work to preprint servers.
1. I just want to get published. I don’t care if the journal has an open access policy.
1. As long as the journal has a good impact factor, open access doesn’t matter.
- data and accessibility impact iportant, but the incentives are still based on IF
- So maybe what we need is an accessibility score rather than an impact factor ;-)
-
3. I want my research to be published in the most prestigious journals only, even if they don’t have open access policies.
4. An open access policy fuels innovation because those who cannot afford to pay journal subscriptions benefit most from it.
5. Scientific publishing will always be dominated by established, commercial publishing houses.
6. I would like to publish in an open access journal but can’t afford the fees.

## Some questions for discussion
- What does open science offer in a resource-constrained setting? And how can the barriers to open science be eliminated?

- The benefits of open science abound and are appreciated and well-motivated, but the pathway towards open science is not. How should that pathway look like?
- Feel powerful in what you have. OLS create that confidence
- A short video on situated knowledge - [Towards Global Inclusivity in Open Science](https://www.youtube.com/watch?v=RRwuOs0BA4I)
- Political and historic issues exists
- Figure the barriers, and seek to break them
- Culture change, which also includes the education system
- Empowering and delegating
- As part of the H3ABioNet Introduction to Bioinformatics blended course, we are introducing learning Circles (Study Groups) in various cities hosting the local classrooms. Each Circle will have a leader; what are some of the tools and skills they would require to be effective open leaders?

- There is the continued growth of and demand for Collaborative research, but cultural barriers ('working in the silos') still exist; how can ECR navigate the culture clash? For example, they may desire to adopt and practice open and collaborative research, but their advisors may not be not open to it...


## Profiles of Panel Members
### Malvika Sharan
Malvika Sharan is the community manager of _The Turing Way_ at The Alan Turing Institute. Malvika works with its community of diverse members to develop resources and ways that can make data science accessible for a wider audience. Malvika has a PhD in Bioinformatics, and she worked at European Molecular Biology Laboratory, Germany, that helped her solidify her values as an Open Researcher and community builder. She is a co-founder of the Open Life Science program, a fellow of Software Sustainability Institute, a board member of Open Bioinformatics Foundation, and a contributing member of The Carpentries community.

### Yo Yehudi
Yo is a Software Sustainability Institute Fellow, founder of Code is Science, EngD student at the University of Manchester studying the effects of community and usability on open source software, editor for the PLOS Open Source Toolkit, board member of the Open Bioinformatics Foundation. They're an open source technical lead at the Wellcome Trust, and previously a software developer at the University of Cambridge, working on an open source biological data warehouse called InterMine.

### Selassie David Opoku
David is trained as a biologist and computer scientist keen to work with the best people and tools to build intuitive and enabling solutions that improve lives, processes, and humanity. His experiences include working with the Eugene Lang Center for Civic and Social Responsibility at Swarthmore College, the Health Division of UNICEF New York, Meltwater Entrepreneurial School of Technology in Ghana, School of Data, Open Knowledge Foundation, and Open Contacting Partnership. His current work through Growing Gold Farms seeks to understand, test, and develop more accessible skills and resources that create sustainable food experience in low-income contexts.

### Peter van Heusden
Peter is a long-standing member of the Galaxy community and is passionate about scientific workflow systems. He is an avid advocate for open source and open science. Peter got into bioinformatics through his work as a scientific systems administrator. Currently mostly interested in pathogen bioinformatics and initiatives that make bioinformatics more accessible. He coordinates a systems and software engineering team, trains as a Software Carpentry instructor and has taught Python for several years, and pursuing a MSc at the University of Western Cape, SANBI.