March 22, 2013

A great role model for collaborative science: meet the OpenWorm

Sometimes even big project could start from a tweet.

A couple of weeks ago I had the pleasure to meet the team of OpenWorm in two live meetings that the they held in the UK.

– from their website:
OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans) [..] With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. [..] 
We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. [..] We are engineering Geppetto, an open-source simulation platform, to be able to run these different models together. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps.
Rigorous predictive models are the cornerstone of science and engineering. Predictive models took us to the moon. Unfortunately, today, there are no comprehensive predictive models of living cells and tissues. Consequently, the entire field of biology and medicine is in a kind of “pre-mathematical” era. A revolution in the biosciences driven by simulation-based research, using predictive models running on high performance computing architectures with flexible user interfaces, is now possible. Simulating a living organism will have impacts on understanding mechanisms of disease, drug discovery and development, synthetic biology, bioengineering, and neuroscience. This is so important to us. 

+Matteo Cantarelli - member of the OpenWorm team - says: "It was 2007 when +Giovanni Idili and I started - naively - talking about simulating the worm. We were approaching the problem after having hit common limits of artificial intelligence. We never got to write any code for the worm at that time, we just had lengthy conversations and paper reading sessions together."

At that time +Stephen Larson was involved in an open-source, 3-D virtual environment project developed by a team of researchers from UC San Diego: the Whole Brain Catalog  About two years after that attempt to simulate the worm with his friend Matteo, Giovanni Idili tweeted on the Whole Brain Catalog's account, these words: "new year's resolution: simulate the whole C. elegans brain (302 neurons)!" - Stephen got the message and for a while he thoroughly pondered this idea.
In fact, Stephen gave a talk @IgniteSanDiego in 2010 where he officially launched the idea. He stated that if we want to get a really high-level A.I. (like Star Trek's Lieutenant Data), we should probably start with a simpler organism.  Even though it is “simpler”, reproducing the functions of C. elegans in a simulation reveals its complexity. The hermaphrodite form has just 302 neurons and the connectome has been already mapped.

After this talk, a lot of people were excited about this idea, so Stephen proposed a survey to reach people around the world who were already interested in this subject. "The key was to find people that were already working on worms and convince them to work together. There are plenty of people around that are excited to do what you have in mind, you just have to find them and show them that working together is better than working separately.." Matteo and his friend Giovanni enthusiastically replied that they wanted to "make the worm". At that point, a series of Skype calls began where the initial team was figuring out the best way to reach this goal. Stephen says: "A good resource that I found useful was  Karl Fogel's Producing Open Source Software free book, which, beyond coding, shows you how to deal with getting started, permission statements, transparency, and so on.. I've learned a lot from this book, and the choice of the name - OpenWorm - was meant to be simple and understandable as they suggest.. "
"There's plenty of science that still happens in non-english language, so that there's still a lot of talent that isn't talking to the rest of the world."
Another serendipitous event was the finding of a YouTube video of a team in Siberia - Andrey Palyanov and Sergey Khayrulin - who had taken the neurons of C. elegans and created a virtual physical body. The team contacted them through the YouTube messaging system because at that time there were no references on the video. At the end they also joined the team.

Stephen: "I realized that there's a lot of scientific communities within Russia and outside Russia that is still rather disconnected. There's plenty of science that still happens in non-english language, so that there's still a lot of talent that isn't talking to the rest of the world. So for us, that was a really great find.."

Then Google +Hangout came in, so they had a broader audience and it was easier to handle conference calls with more people.
They currently meet every two weeks on Google hangout. A great practice they have is to discuss high profile papers related to the simulation of biology with the authors, and stream the talks on YouTube. You can take a look on this Journal Club on their channel.

Stephen, Giovanni, Matteo and Mike @+OpenWorm Live in Cambridge, UK
Matteo: "At the beginning it was Stephen, Giovanni, Tim and I, if I remember correctly. First, I started building an ontology with Stephen to try identify the high-level requirements for simulating the worm. What was needed, what physical aspects we had to simulate and to gain a better understanding of the big picture. After that I worked to transform the requirements we gathered into technology by designing the architecture of the simulation engine, what we recently named Geppetto, and took a first stab at implementing the different modules. During this time Giovanni was writing the first module for the simulation engine with a proof of concept of a simple Hodgkin-Huxley neuronal simulator that leveraged GPU".
Stephen: "Other people eventually joined the project. Christian Grove from Caltech who contributed with the 3-D rendering of the worm. Then, a group from INCF,  from which we decide to use NeuroML, a standard language for the model, so then we get connected to the NeuroML community where more people came to the project." He also stressed the concept to have an organizational structure, for instance OpenWorm is structured like the Bazaar theorized by Eric S. Raymond, where there's a central coordinating platform but it’s actually run by a series of sub-project that has a common direction.
“Chance handed me a perfect way to test my theory, in the form of an open-source project that I could consciously try to run in the bazaar style. So I did—and it was a significant success.” -- from The Cathedral and the Bazaar by Eric S. Raymond
OpenWorm 3-D rendering
" start to write down on a piece of paper all the things that comes into your mind, and you try to connect them, and all the aspects between them. When you do such a brainstorming you might realize that some stuff are related, and that this and that could be grouped together. So, if you're creative enough, you start to find some larger theme that cover all this stuff, and that gives you the ability to work on all the things you're actually interested in at same time..."

Stephen gives other suggestions to people that wants to commit themselves in a collaborative project. I think that his suggestions can be true for - pretty much - any young scientist who wants to approach this kind of career without being disappointed at the end of the day. In my opinion this could really work in general for any scientist.  "I think you got to find something that you're truly excited about. [..]  I think that the challenge early on is that is really easy to be excited in something for about two months and then you give up. It means that probably you're not really interested in it, or you can try to discard this idea for a while and return back on it later. Sometimes stuff works better later."
So, after you have done your homework, you start to write down on a piece of paper all the things that comes into your mind.  When you do this brainstorming you might realize that some things are related. [..] and you may start to find some larger theme that covers all this stuff.  That gives you the ability to work on all the things you're actually interested in at same time. For me OpenWorm turned into that. I was interested data visualization, artificial life simulation, neuroinformatics, something that is biologically relevant... but there was a lot of things in my previous projects that didn't actually allowed me to stretch into all these topics. OpenWorm was for me the key project to focus on all the things I was truly excited about at the same time."

OpenWorm is made of many other people, most of which aren't mentioned here. But all of them are incredibly committed to what they're doing. I think that this is one of the best projects to join if you'd like to work with skilled people with a genuine passion for Artificial Intelligence. OpenWorm is definitely something that is truly visionary.

Part of the OpenWorm team and fans @+OpenWorm Live in London, UK
"All the code we produce in the OpenWorm project is Open Source and available on GitHub. This makes it easy for everyone to look at and play with.
Detailed documentation for each sub-project is available from the Projects page."

Varshney LR, Chen BL, Paniagua E, Hall DH, & Chklovskii DB (2011). Structural properties of the Caenorhabditis elegans neuronal network. PLoS computational biology, 7 (2) PMID: 21304930

Palyanov A, Khayrulin S, Larson SD, & Dibert A (2011). Towards a virtual C. elegans: a framework for simulation and visualization of the neuromuscular system in a 3D physical environment. In silico biology, 11 (3-4), 137-47 PMID: 22935967

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