Fatma Guerfali “I'm a biologist doing bioinformatics work — without this kind of openness in science, I wouldn’t be able to do what I do.”

Fatma Guerfali is an Assistant Professor at Institut Pasteur de Tunis and an Open Science advocate. She has been active in the internet health movement as a Study Group Lead. She co-leads a Study Group in Tunis, and as a Mozilla Open Leadership Cohort member, is actively mentoring others to work and lead in the open. She is involved with H3ABioNet, a Pan-African Bioinformatics network comprising 32 Bioinformatics research groups, that is developing bioinformatics capacity within Africa. Her contributions have helped others in her community, and her associative activities have helped girls and young women, learn the skills they need to participate digitally, and her efforts have been critical in opening research practices to communities that do not have regular access to teaching resources.


Fatma’s Story

Start by giving me an overview of your work and your goals.

I’m working in Institut Pasteur in Tunisia. I have a background in biology, but I’ve been working a lot on big data, particularly for generating high-throughput sequencing datasets for parasites and for human samples infected with parasites. We’ve been working a lot with these kinds of big data, so I moved a little bit towards bioinformatics and now I’m also teaching bioinformatics in separate courses worldwide. This is mainly done in the context of EMBO (European Molecular Biology Organization) courses or within the network of Pasteur Institute.

Throughout my career, I’ve faced several difficulties in finding the competences to do the right thing at the right moment. When I moved to Mozilla study groups, it was interesting and important for me to talk to colleagues, friends, and different people in different workshops — where we have the opportunity to present our work and meet people. It was really nice to interact with these different backgrounds.

I started to see that the problem arises from people sticking to their own competence and their own background — they do not really feel comfortable going to see other people and talking to them. Even worse, nobody tries to understand what they could to do for others, and what others could bring them. In my case, I’m a biologist working with large-scale datasets,  so I can’t possibly imagine doing my work without talking to a statistician or a computer scientist. I cannot go to them with pre-existing big datasets to ask, “What can you do with it?”

I know a lot of biologists that make that mistake. When everything is done, you can’t go back — these are things that cost a lot of money. The statistician will tell you, “No, it’s too late. You haven’t done enough replicating, it’s not useful. We could still work with your datasets, but the interpretation would be biased.”

I started thinking that the best way for me to do my work in the right way was to learn a bit about what others that I would call “complementary scientists” were doing. We don’t have the ability to pay by credit card from abroad, so I’ve been using the many useful and free tutorials out there on the internet — I followed several courses on bioinformatics and been practicing a lot my new skills on my own datasets. I’ve since then moved to bioinformatics and have been teaching  courses abroad. I’ve learned what statisticians and bioinformaticians can bring to my research.

I started a Mozilla study group because I wanted other students, the youngest generations in Pasteur Institute, to feel connected and supported. There can be a lot of competition between different groups, but Mozilla study groups is something that allows you to bypass all of these problems and create a small community of people. They don’t necessarily always work together, but they are at least sharing their competences.

When we started the study group, which was primarily comprised of biologists, they feared the concept of open science. They had problems understanding it because they usually work with sensitive datasets — data associated with human patients, so they can’t give out information about that — which is understandable. The Mozilla study group isn’t about giving away your datasets for free and we had a problem explaining this.

That was one of the major challenges we’ve faced — explaining open science to our colleagues. If Mozilla could give real-life examples or success stories about what open science can bring, I think that would help — this could be a document or website where everybody could share and give their opinion based on their own experiences.

Despite this challenge, we were able to bring people together. We didn’t start working directly on datasets at first, because we felt that it was necessary to spend some time arranging tutorials for people to achieve a minimum level of bioinformatics. We’ve been trying to give any participant the opportunity to have the same basic skills so that each time we meet, we could be working on common interests. We wanted the youngest generation to be aware of what exists and the potential they could have in using these kinds of skills.

Another important thing for us was to bring this young generation of scientists, of researchers, in a common group so that they get to know each other. Sometimes, you can work in an institute or organization and you don’t know that your neighbor is doing the exact same thing as you. You’d usually go to the internet to see different publications and try to find out who is doing it — but you might not know that your neighbor is doing it.

In the beginning, we gathered everybody that was willing to participate and had a meeting featuring the names of each participant — each highlighted their competence and what they were expecting to get out of the group. Based on that, we organized different sessions and defined a project that would interest the majority of people.

There was a conference for young scientists in Tunis, at Institut Pasteur. It has been organized by young scientists, mainly for young scientists — but, of course, everyone was invited. We got a slot to present the Mozilla study group, the options, what we do, and what we are willing to do in order to gathermore people.

At first, people were afraid of sharing data, but then we said, “Yeah, but we could use public datasets.” The idea is that you share your competence. Then people really started understanding the benefit of sharing competence, not just for credit.

The interesting part of Mozilla study group was that you don’t only get to know the other competences that you have on site, but you understand that science is about sharing. It’s also about sharing for free. It doesn’t really matter to have your name on a publication just because you managed to explain something really simple to your colleagues — something that took a half an hour of your time, and thatsaved someone a lot of time and effort in trying to figure it out.

It’s a human thing, it doesn’t really have to relate to research. This was something that interested me a lot in Mozilla study groups. You have the human dimension, you have the collaborative dimension, and you also have the research dimension because you could collaborate with other people. These are the main points.

Another important thing was that we got to know each other, and this allowed us to create a small community within the community. It’s really nice for the youngest generation — they have this ability to talk to each other very easily. These groups create a kind of platform for them to talk to each other, to understand who is doing what, and how they could complement each other.

This is especially true for us in Tunisia. People study in university throughout their curriculum, but they get most of their competencies through trainings abroad or spending time in another lab. They develop their skills on the go. The study group and the study guides we created will enable this new generation to learn faster. We have the ability to go to training, but you can’t go to ten trainings a year, so if you have that competence just next door, why not use it?

It’s the presentation of the research and what people are working on or of their datasets specifically?

We did both. We had the first meeting where people were saying, “Ok, this is my name, this is the thing I am doing, I am an expert in this, I could share, and this is the thing that I would like to understand, learn, or that I would like you to cover.” We’re not always the trainers, so we identify the competencies among the young people and we match the needs using this big table.

We also participated in the Mozilla Sprint, so different researchers from different backgrounds and levels of expertise came together and we all worked on the same project. We were among one of the most active groups!

However, a big challenge is keeping everyone interested and engaged. Although it’s not expected, it would be great. If the group is working on a specific project, and it doesn’t really relate to your work or you don’t have the expertise or the need to do it, that’s fine. You can stick around and help out with the current project, or you can wait for the next project to begin. The problem is that if people spend two or three months without coming, they get disconnected. We try to keep them engaged by sending out emails and keeping up communication. It’s a bit difficult to have one common interest for everybody and to keep everyone updated.

So there are community engagement challenges?


Thinking about this work that you’ve been doing, can you give me an example of a specific time where you’ve felt a sense of success?

When we all worked together at the Mozilla Sprint. We gathered in the same room to sit and work on a project together. We brought in pizza and drinks and worked for two days. Everybody could come and go, and share and implement ideas, correcting things as you go along — all in a shared document. We discussed what was important for us to implement as a group. With these kinds of initiatives, you get rid of all of the boundaries and limits that you usually have between different labs or different research groups. The only focus there was on science.

People are able to step outside their comfort zones and show their personality when sharing their thoughts and ideas. This is not common practice within the workplace. It’s not easy to find the kind of initiative that would allow you to go beyond what is expected of you for your work. This is something that you can really do for yourself, while at the same time including others.

It’s kind of a systems thinking — you understand what the other needs are, you start working in a community. There are a lot of researchers that work on their own because they have specific research subjects, but this kind of initiative gives you a place not only to work with different colleagues on different things, but also to talk about science knowing that science is not the only thing you do everyday — you go a bit beyond your normal frontiers.

The document that you were working on, was that a specific project?

Yeah, there were different projects that Mozilla Science proposed and we picked one of them. There were a lot of projects that were related to advanced science and how to implement pipelines — research-based things. However, our group had different levels of abilities and we didn’t want the young people to be upset about not being able to contribute, so we decided to work on something a little more broad called, “Open Data Training.”

My next question is about getting an example of a challenge from you. Looking back on what you mentioned before, is there one you’d like to hone in on or do you want to give an example of something else?

The biggest challenge is to hold people’s interest throughout the year — getting people involved and doing it as an act of community engagement. At the beginning, it was difficult to get people to understand that they should not only come when the subject is interesting for them or when they want to learn something specific — that they can come even if they know everything about that tutorial because they can help friends. It can be difficult with scientists — many might have the interest, but think that it might be a waste of time.

I’m understanding that people will come if they feel like they have something to gain, but are less likely to come if they only have something to give.

Yeah, though I don’t think that’s true of every scientist.

Right, ok. What are some of the ways you’ve approached addressing this challenge?

We try to take the experts at different levels of expertise and have them do the tutorials themselves for those that require to learn their skills. This is a way to interest advanced people who might get bored if we were to always do the training — telling them things they already know. It is a way not only to give each category of people the help they need at their own level, but then also a way to make them contribute to the community by giving back what they’ve learned to the others.

We also try to convince people who come from different areas and labs to come together and teach a course on the same subject.

You’re bringing people from multiple labs and having them collaborate on the tutorial.

This is what we try to implement at least.

Has been working for you in order to address this challenge? In some ways, it’s convincing people about the benefits of giving. Have you gotten any feedback? Have you seen change in attitudes? If so, have people reported to you about the benefits of giving?

Yes. We’ve gotten a lot of thanks. They’ve said, “We feel like, now, we can be more confident in doing this kind of analysis and using the tools that you showed us.”

For the next season, we have decided to do a more advanced level tutorial — a complement of competence, expertise, and skills to give to people that are advanced in one particular subject. Then, have the advanced people take that knowledge to another course or another session or group for their colleagues who are less advanced. It was an idea we came up with through group thinking in order to make sure that everybody at each stage would be involved no matter the competence, and no matter the skills.

What I’m trying to hone in on is what are people gaining from contributing? Why, if I’m advanced, would I spend my time teaching others?

You are participating and giving back to a community that gave you something — the opportunity to advance yourself. You are also a part of a community that could give you help. We are showing people how to see it as a win-win strategy. If you had the chance to learn from someone else then you should use whatever chance you have to give back. This is what open science is about.

In any kind of category, in any kind of job, there are always people that do not want to share their skills. We try to get people to understand the concept of open science, so we spend two or three sessions at the very beginning to explain and have discussions about it. We want people to understand that this is a win-win strategy.

Turning now to the broadest issue in the Mozilla universe — which is keeping the web open and free — what, for you, is the open internet?

We are living in a world that is so full of datasets and information. Things are going so fast that it’s not really possible to work on your own and stay relevant. If you share and have the support of your colleagues or even other people that you don’t really know, you will be able to go further, faster. I’m a biologist and I’m doing bioinformatics, but that doesn’t mean I’m an experienced coder. I’ve been using GitHub or similar resources that have been developed by others for the community — they have that competence. Without those resources, I wouldn’t have been able to go as far in my analysis. I’m a biologist doing bioinformatics work — without this kind of openness in science, I wouldn’t be able to do what I do. You can work on your own, but you’ll only be able to go a meter. When you collaborate within open science you will go a hundred kilometers.

It’s important to keep in mind, when talking about open science, that even if you have a skill or competence you’ve acquired through your own experience or efforts, you should still share it — it’s part of giving back. You had a chance to acquire those skills because at some point you were given that opportunity — your parents had enough money, you could go to school, you had the ability to take different courses, you have any kind of competence. There are so many people who don’t have the same opportunities, but that doesn’t make them any less intelligent. They are really amazing people. They just need an opportunity — a little help — to be really efficient in their work, so why not give them that?

Within your group, is this a value and rationale that resonates with people?

Yeah — for our study group and also in our lab group. We insist to anyone that wants to work with us that it’s important for us to share everything. We are all listed in our publications because we all helped at some point with something. In biology, bioinformatics, or whatever field, if you have a colleague or know someone with a specific skill — ask them to help — there is no need to waste your time trying to learn that specific skill. You can advance faster together than on your own — this is true for any kind of work.

Getting more specific about Mozilla, how did you get involved with them? You’ve already talked a little bit about what that’s been like, but maybe we could dig deeper into what that experience has been like for you.

I met the Mozilla group for the first time in Berlin. I’ve been in the community thanks to my colleague, Amel Ghouila. She will be able to tell you more about it started. Her background is in computer science — she’s an informatician. She’s more involved in the GitHub thing and these kinds of communities. We share the same office and have been working a lot together. Some of my most successful work has been done with her because each of us is bringing expertise from our respective fields — that doesn’t mean that I’m doing her work or she’s doing my work. I understand what she can do and she understands what I can do and that allows us to collaborate very easily. She was the one who told me about the Mozilla study groups and asked if I’d be interested in developing one. This is why I’m here, thanks to her.

What I’m hearing is that it’s been a very satisfying, collaborative experience for you that advances your work, but also has human and social community sides to it that lift you up. I don’t want to put words in your mouth, but that’s what I’m hearing.

I’m a scientist, and I’m really into things about sharing. This might be a little too philosophical or psychological, but that’s the way I am. I’m someone that doesn’t like competition for competition’s sake. I dislike people that don’t share things. I don’t want to live in a community that has competitive high schools — where you don’t show your work to your colleague because you want one point more than they have. I hate these things, and dislike these kinds of studies where you have too much competition — it’s an awful environment for me. It’s really important to have the opportunity to go beyond the simple science we’re doing every day — to bring a little bit of humanity into my workplace.

Tell me about a time where your involvement with Mozilla or science labs didn’t meet your expectations. Do you have some feedback? You already gave the example that it would be good to have some support in terms of explaining open science, perhaps a common document or set of points that people could keep updating and draw from. I’m wondering if there are other pieces of feedback or other ideas that you have that we can share?

Not really. There is good communication within the community. There’s that Gitter Notifications opportunity to communicate where people talk to each other. We email and have group discussions. Keeping up to date about what is going on is really important, however having a discussion is just as important because it gives us a chance to give and get feedback from others.

You’ll read funny things sometimes from people getting bored from getting too much and not having enough credit. I remember when Stephanie posted a guy’s comment complaining about the fact that he was developing really good things and someone from a private company took it. It was a pity for him because they didn’t give credit to the one who developed it. The need to cite the source is one of the main concepts of Open Science. I was commenting on that saying that there are so many things that we’re using in our everyday life and we don’t even know who invented it.

These are things that have been invented like one hundred years ago and we don’t really know who the inventor is — who invented the wheel, who invented the spoon, I don’t really know, but we’re using them. We’re grateful to them for doing it. It comes down to why you are doing it. Are you doing it for yourself or for the community? This is something that is not always clear. I can completely understand that one guy who spent a month developing something that would be used by a private company is not really nice. But if there are one hundred people who have also used your work and got benefit from it, that’s worth it.

I don’t know what the licenses are like in this example you’re giving. The license that I tend to use a lot is Attribution Share-Alike, which is an open knowledge license. It basically means that you can take what I’ve used, but you have to credit me and anything you make with what you took, you have to share it in the same way.

This is really nice. It really needs to be shared among the community!

It creates a chain. There’s a number of open licenses out there. This one is called Attribution Share-Alike. You could also add a noncommercial element to it, but then it doesn’t make it open according to the Open Knowledge Foundation. The only licenses, at least within the Creative Commons framework, that give up ownership are CC0, where you put it in the public domain. We’re not talking about putting stuff in the public domain, we’re talking about openness and there’s a lot of misunderstanding about that. If he had used a license like that in this case, that company would still be liable. What they did was not ok.

Exactly. This is something that definitely should be stated in the document about open science that we were discussing. The thing is, there’s still the possibility that another person or company takes your script, for example, or your code and develops based on it. If they add or remove things, that is easy and it doesn’t look like your own. This is a bit more complicated because even if you sue them, they would say, “Ok, we’ve modified it anyway, so it’s not yours.” It’s a bit complicated for people to be able to understand that, so I would really appreciate if this could be included. I’m using Creative Commons when making presentations, but there are so many other things going around and I don’t really know them. It would be nice if you could share this information through that document and specify these possibilities.

Absolutely. The Open Knowledge Foundation has a whole page of licenses beyond the one that I mentioned that they consider open.

That’s nice.

Yeah, I’ll share that with you.

Thank you so much. If you could mention it to the Mozilla group, that would be nice.

Absolutely. Just two more questions. We’re collecting these stories from all around the network from other people working in science, from open web fellows, from news, from people working on web literacy. How might the stories that we’re collecting, if at all, be useful to you?

I would go for small quotes from everybody. Just two sentences that everybody could easily understand. Reading the different openings would be nice. Do you know that story about an elephant. You bring an elephant to three blind people and each person believes it is something different. It’s all the same thing, but everyone has a very different perspective — each person giving his own opinion and they can only get the whole picture when bringing together their opinion

What an issue is or what a concept is — yeah. Finally, is there anything more you want to tell me or ask me?

I’d like any information about community engagement or nice ideas from different groups worldwide. I’d like to know about any specific, bright idea about how to keep things going, how to interest people, and how to make them work as a community. If any of this could be shared, it could give other groups some great ideas. These are things that you don’t even know they exist because they are within group organizations. It’s a way that groups keep going and they sometimes have very interesting ideas, but we don’t really know about them. If, through the Mozilla community, they could share tips that would be nice.

Mozilla is really good at this, so that’s a good piece of feedback — that community engagement tips and practices would be really helpful. What you’re also talking about is communities of practice and how to keep those going — Étienne Wenger knows a lot about this. Because I’ve also done a little bit of this work, I’ll let Mozilla know, but I can also pull together a few resources for you on that.

It would be great to have feedback from different communities. Mozilla study groups are running in different countries, but each country has its own mentality, different ways to interest people. These people have different backgrounds and they do not always have the same chance of having the same skills, so each one in his own community is facing different kinds of problems. It’s also nice for the Mozilla community to know that so that they can help more people who need help instead of discussing the same way with different countries. This would be a loop. The community having feedback from other communities and applying the one that would suit their needs, but also giving back their own concerns to the Mozilla community so if other groups in the same country are opening, they can make people communicate and talk to each other.

Do you envision this between science groups or between Mozilla groups more broadly — like people working on open news or people working on advocacy?

I would say broadly just because you can learn about different perspectives.

Great, well thank you very much.