Podcast: Can supercomputing speed up the race to find a Covid-19 vaccine?

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Finding a vaccine for Covid-19 is a medical emergency. Could supercomputing speed up the race to develop a vaccine against the SARS-CoV-2 virus? In this podcast, Esade Associate Professor Esteve Almirall talks with Alfonso Valencia, director of the Life Sciences department at the Barcelona Supercomputing Center, about the potential of computer science to speed up the race to find a Covid-19 vaccine.

PODCAST TRANSCRIPT

Esteve Almirall: Today we're fortunate to have Alfonso Valencia with us. He is a Spanish biologist and computer scientist, a great professional and the Director of the Life Sciences Department in the Barcelona Supercomputer Centre. He is working on a number of Covid projects including collaborating with one to create a vaccine. His curriculum is truly impressive with more than 60,000 citations, more than 400 papers, among articles published in Nature, Nature Genetics, Bioinformatics, Protein Science, and many more. In 1994 he created the Protein Design Group within the Spanish National Centre for Biotechnology and from 2015 to 2018 he was the President of the International Society  for Computational Biology. Since then he is leading the Computational Biology Life Sciences Group at the Barcelona Supercomputing Centre. Professor Valencia, it’s an honour for us to have you here with us. Thank you.

Alfonso Valencia: Thank you.

Esteve Almirall: We are so happy that you have a bit of time for our Esade podcast. We know that you're involved in a fantastic new project about finding a vaccine. What can you tell us about that?

Alfonso Valencia: Vaccines are the "holy grail" of our time, as is finding a vaccine against the Covid-19 epidemic. We are part of a large European consortium trying to find a vaccine and working for that. Obviously, we do the computational part, the prediction of the antigen side, the initial modelling required to design the vaccine. And then this goes into cycles of experiments and more computing and running. There are many of these projects running around the world. It's a big collaborative effort and we will hopefully have not one but a number of vaccines ready on time if there's a second wave or for the next epidemic.

We will hopefully have not one but a number of vaccines ready on time if there's a second wave or for the next epidemic

Esteve Almirall: There’s a lot of pressure on having a vaccine fast, on the timeline. What is your view on that? Is modelling with supercomputers going to make having the vaccine faster? Are they pushing this timeline closer? What do you think?

Alfonso Valencia: Science doesn't have a given time. Science is about trial and error, so we cannot say how successful we are going to be. But certainly we, and the other projects running in parallel, are being careful to try to speed up the process that, by definition, takes time because you have to cover all the phases from basic research to production, to mass production. Computers are completely involved in this, from the very first design phase to the large-scale organisation of the production system. So I think it's not only that the computers can speed up the processes. I cannot imagine how you can do a big project with a lot of data and complicated areas without computers.

Science is about trial and error, so we cannot say how successful we are going to be

Esteve Almirall: You’re a biologist but you don't work in the lab. How can you simulate all the reactions that are normally present in the lab? And why do you need a supercomputer for that, or do you need more than a supercomputer, a "megasupercomputer"?

Alfonso Valencia: We cannot simulate everything that’s done in a lab. Life is extremely complex, and our understanding of the basic science level of life is still relatively small. So all we can do in terms of simulation is simulate what we understand – a small part of biology. Still, this small part of biology that we do understand can be processed on computers and this is why we have a big supercomputer, MareNostrum. It is one of the largest computers in the world. We are also buying a new MareNostrum computer that will be a hundred times more powerful than the current one. This will help us to interact with experiments, to prepare things that will later be tried in an experimental lab. Then we’ll determine the fit with this information and go back and forth between models and predictions, and experiments and biological results in what is, I would say, the “big challenge” and the unifying space between experimental and computational science.

Esteve Almirall: Many times we face this dilemma between open science and intellectual property. This is probably a difficult issue in many firms but particularly in the bioinformatics field. Are the programmes and the models that you use open source? How do you manage to work around all these issues?

Alfonso Valencia: On the contrary, for us, it's very easy. Everything we do is open source, the software and the data. Our area is very much inspired by the Human Genome Project and, from the very beginning, fortunately, it has been driven by completely open collaborative science. So all the sequences, all the large-scale sequencing that goes on around the world is being done, obviously, with the appropriate restrictions regarding ethical issues and trust permissions, but all the information is open and accessible. All the software that we produce and that the editor of the main journal in the field will publish has to be accessible and completely open. So for us, it is not much of a dilemma. We just do everything in open.

We are facing such big problems, on such a large scale, that we need to bring together all the resources that we have

Esteve Almirall: Your team is a public consortium. You have governmental organisations and you collaborate with private companies such as Grifols, IBM, amongst others. Organising all these must be complicated and probably a little bit more so in Spain. What is your experience? What is your view of these public-private collaborations? We know that you are also a member of the Scientific Advisory Board for the IMI [Innovative Medicines Initiative]. What can you tell us from this point of view?

Alfonso Valencia: My view is that we are facing such big problems, on such a large scale, that we need to bring together all the resources that we have. We know that, in the area of medicine and new drugs, pharma companies are the only ones that can really produce new drugs in a significant way. Interesting things can be done in the experimental lab, but, at the end of the day, the production of drugs is extremely expensive. So we need collaboration. It is not only the price but also commercialisation, the expertise, the big high-throughput technologies. So, in this area, I think it's essential and that is why the European initiative for new medicines, IMI, has been working for years and I would say in a very successful way, bringing together public and private resources.

In a small way, the same thing happens in the area of IT technologies. The big IT companies are the ones that have the capacity to produce large-scale computers like MareNostrum. So we need the computers and we need the collaboration. And this collaboration has to be done in a fair way, meaning that we have to produce something that is good not only for the company but also for society in general. I think that maintaining the equilibrium, the right balance between the profits of the companies that are part of the society and the societal benefits, and doing this in a completely open and transparent way is very much the way forward, the way in which science and technology are moving these days.

I cannot imagine a future in which we have another epidemic and cannot benefit from all the technology based around mobile phones, positioning and communications

Esteve Almirall: Now, we also hear a lot of talk about tracing apps and this tension between having enough data to make them useful, an adoption rate by at least 60-70 percent of the population, and privacy. Some might say: “We don't have enough data; it’s not effective. But we also have to maintain privacy.” What do think about that? Are Asian countries doing it better than we are or is it better to let everybody to obtain it?

Alfonso Valencia: This is an interesting and very controversial area. First of all, looking to the future, I cannot imagine a future in which we have another epidemic and cannot benefit from all the technology based around mobile phones, positioning and communications. Now, we can discuss if the technology is right, if it is ready now, if it is not ready now or what the problems are. But in 10 years, it is difficult to imagine a world in which there will be no benefit from this technology. So we better start learning how to use it, because it's going to be there because it's very powerful.

Second, there are all these efforts to trace cases. There are human teams doing that. I can imagine that the teams will benefit a lot from being able to trace the contacts that cannot be traced by humans on their own – contacts in the past. You cannot do this; a human cannot remember all that. So you need something else. I don't see why we cannot benefit from this technology.

My second controversial point is that we are now, very likely, at least in Europe, heading towards what is called a decentralised system. A decentralised system means that the government has no idea, no control, no data. I cannot understand that because the government, meaning the healthcare system, already has all my information, all my medical records, everything about me. They can call me on the phone to say I have an appointment tomorrow. So why can’t they have my data on something like Covid-19 for which it is even more important to have this complete data? I fail to understand why it’s better for Google and Apple to have this data and not my healthcare system. So, maybe I’m an "outsider" in this, but at least I'm voting for my government. So doing this… at least I trust my healthcare system, and my data is already there.

We need to use digital technology if we want to be able to really trace contacts

So, in this sense, my view is that a centralised system would be better. The technology is there, and there are many things that we still don't understand well about the technology. We are managing the figure of 60-70% of people using the app. We just published a paper trying to understand where this number comes from, because it is not very clear where it originates and what the conditions for this figure are. So I think there are many interesting scientific and technical questions that we still have to resolve. But we better find out soon because we need to use digital technology if we want to be able to really trace contacts.

Esteve Almirall: What can we do to promote this science associated not only to this immediate thing, but also to this long-term vision?

Alfonso Valencia: Obviously, I understand, in a sense, this social push to have benefits as soon as possible, even more so these days with Covid-19. At the same time, we know that this is something that is happening now, but you want to build the bases. If we had invested in improving our understanding of viruses and ecosystems, and the transmission and physiology, we would be in a better position right now. Now we realise that we don’t understand some of the bases, but how are we going to create a vaccine if we don't understand some of the molecular bases? So, we are really facing a shortage in terms of basic knowledge.

If we had invested in improving our understanding of viruses and ecosystems, and the transmission and physiology, we would be in a better position right now

This basic knowledge is not something that can be controlled and produced within a given time. We need to try a number of things, a number of projects. Instantly progressing is intrinsically difficult. We need to realise that we need fast solutions but that these fast solutions are based on basic knowledge and cannot be generated any other way. We don’t know any other way of working on this in many different areas and building this basic knowledge that we need.

Hopefully, thinking, dreaming of the future, all these pandemics and all these discussions will help us to make scientists and their importance more popular in society. Scientists have appeared in the media more now than ever before, more than a football player now that footballers aren’t playing. Obviously, this will not last for very long and we will be replaced again by football players in a few weeks. Hopefully, we will not be completely replaced and will still be reminding society about the importance of science just like the importance of a strong public healthcare system and a strong public education system.

Hopefully, dreaming of the future, this pandemic will help us to make scientists and their importance more popular in society

I’m optimistic. I think that people have already realised that there are many things that we want to know and that we need to know. And, also, they have realised the big difference between the societies that have really advanced into the 21st century and societies where things have not quite advanced into the 21st century. I think that the big technological differences that we see between some of the Asian countries, in some of the European countries and other countries are in good part due to the investments that they have made in science and technology over these years.

It's not impossible. They have done this in a very short time. So it’s not that we are lost; we can still do it. But we need to really decide to step forward and consider size, not only the "nice" accumulation of knowledge but as something that is essential for things like epidemics and also essential for building a knowledge-based society. And this is more than worth all the technology that we are developing. And, going back to the app and contact tracing, all the technology behind cell phones is based first on basic knowledge and then on technological development. And then this leads to the companies that are the largest companies in the world today. I think that the path is there. Other countries have done it. They have done it in not a very long time. So all the elements are there, and I just hope, dream, that society will learn from all this and take this step forward.

Esteve Almirall: Oh, let's hope so. Thank you very much again, Alfonso, for being with us these minutes. We know that you have a really busy schedule.

Alfonso Valencia: Thanks to you. Absolutely.