I am currently thinking about starting a very niche passion project about genomics. A kind of biological version of assembly, or more precisely a human-readable version of the genome. The aim would be to give SWE the ability to edit “genomic code”.
However I am in great pain to find who to talk to. I an beginning to ask myself if it’s because I am doing something the wrong way, or if it’s because there are no needs for such a tool…
Lots of cold emails and cold reachouts on LinkedIn/Twitter/Threads probably. Checking out research lab websites in universities like UC Berkeley is probably a good place to start.
University of Pennsylvania has some projects that include public providing help with genomic/epigenetic research related to given topic descripition[0]. (using l-systems & bnf[5][8][9] format as way to encode/handle dna sequences [1][2][3][4][6][7])<p>Example/demo of topic : [10]<p>[0] : <a href="https://genetics.med.upenn.edu/" rel="nofollow noreferrer">https://genetics.med.upenn.edu/</a><p>[1] : automated dna motif discovery : <a href="https://arxiv.org/abs/1002.0065" rel="nofollow noreferrer">https://arxiv.org/abs/1002.0065</a><p>[2] : Improving CUDA DNA Analysis Software with Genetic Programming : <a href="https://dl.acm.org/doi/10.1145/2739480.2754652" rel="nofollow noreferrer">https://dl.acm.org/doi/10.1145/2739480.2754652</a><p>[3] : <a href="https://link.springer.com/chapter/10.1007/3-540-48304-7_21" rel="nofollow noreferrer">https://link.springer.com/chapter/10.1007/3-540-48304-7_21</a><p>[4] : <a href="https://web.eecs.umich.edu/~weimerw/p/weimer-tse2017.pdf" rel="nofollow noreferrer">https://web.eecs.umich.edu/~weimerw/p/weimer-tse2017.pdf</a><p>[5] : <a href="https://github.com/shnewto/bnf">https://github.com/shnewto/bnf</a><p>[6] : <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194197/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194197/</a><p>[7] : <a href="https://www.biorxiv.org/content/10.1101/088930v1.full" rel="nofollow noreferrer">https://www.biorxiv.org/content/10.1101/088930v1.full</a><p>[8] : <a href="https://en.wikipedia.org/wiki/FASTA_format" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/FASTA_format</a><p>[9] : <a href="https://www.mdpi.com/2624-6120/3/4/42" rel="nofollow noreferrer">https://www.mdpi.com/2624-6120/3/4/42</a><p>[10] :
a) <a href="https://discoveringthegenome.org/" rel="nofollow noreferrer">https://discoveringthegenome.org/</a><p><pre><code> b) grape : https://www.mdpi.com/2624-6120/3/3/39
c) needs 3d printer extension for real world replication : https://bnfc.digitalgrammars.com/</code></pre>