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Calling all biological and biochemical researchers, we need you!
We are working with Harvard and want to learn from, you, the community of researchers working on biological and biochemical problems, about the bottlenecks that we are likely going to face as we move toward producing a reliable computational simulation of a biological system, and are asking for 5 minutes of your time to complete this survey.
We start with the assumption that, in order to simulate a biological system, a complete understanding of all the intra and inter cellular communications or molecular interactions (proteins, silencing RNAs, receptors and their ligands, cytokines, antigens, etc) is necessary. Not only will we need to know “what” molecular interactions are possible but also “when” and “where” they occur, “how” they are carried out and what happens when they do.
There are several ways that we could look for the relevant information:
1) Searching for the measured proteins in scientific literature is the most common method yet it is time consuming and important studies can be easily missed;
2) Databases curated from literature exist (e.g. Reactome, KEGG, ingenuity pathway analysis (IPA)) however they are often several months to several years behind the state of the art, which means we still need to use 1);
3) Automated literature extraction tools can be used but given the lack of specificity and type of experiment, those often have too many false positives again forcing us to go back to 1)
The results of the survey will be used to help us understand whether there’s a need to capture those interactions in a more systematic way during or shortly after publishing and, if so, what type of data supports the truthfulness / quality of the information. The survey is completely anonymous, very short and we will be very grateful if you could share your opinion with us.
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