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\begin{document} \section*{Feb 6 Update} \subsection*{Orthologs} \begin{verbatim} I have all of the orthologs mouse to zebrafish orthologs for a while. Recently I did a bit of processing and narrowed the list down to just one to one orthologs since that seems to be what the Clark paper wants. \end{verbatim} \subsection*{Paralogs} \begin{verbatim} This is the section I have had the most issues with. I initially relied on a fetch all paralogs method from ensembl but that cut out before it was done. So I went in and pulled paralogs for each unchecked gene individually, thinking that I would add this new set to my pre-existing set. There were two issues with that idea that I discovered recently. Firstly, that method also was interrupted prematurely by the server cutting my connection. Secondly, and more dire, this gene based paralog fetching seems to pull far more paralogs per gene. That worries me, since I want a consistent method of evaluating what is and what is no not  a paralog. Currently I am running a test script that should allow me to limit paralogs to only the most highly related pair. \end{verbatim} \subsection*{Annotations} \begin{verbatim} I used the Gene Ontology website to get their annotation guide and the annotations for mice and zebrafish. I also went through the annotation and selected for only those annotations that experimental support and focus on the processes outlined in the clark paper. \end{verbatim} \subsection*{General Work} \begin{verbatim} There has been a lot of hurry up and wait for a long time so I've been trying to prep myself for future steps while I wait for programs to finish. There has been a lot of learning and relearning Ensembl's API. I have also been learning python and practicing with it for when I get the scripts. I also have been reading papers on Phenoscape and Phenex and am starting the process of learning all the languages and API's I'll need to work with Phenoscape. \end{verbatim} \end{document}