Orthogonal Research: quarterly report (4/2 to 6/30)

1) Alife XIV conference (5): * Alife XIV Program Committee activity: three papers reviewed. * Alife XIV Paper Submission: "Market-Mediated Economic Value" paper accepted as poster, paper withdrawn due to lack of travel funds. Paper remains live at arXiv. * paper presentation being created (will be posted to Figshare when completed).

2) Biosystems manuscript (1): * “Toy Models for Macroevolutionary Patterns and Trends” accepted: two rounds of revision, paper accepted, proofs completed (with Richard Gordon). 3) Blogging, Fireside Science (3): * three post series on Meta-Science: “The Structure and Theory of Theories”, “The Analysis of Analyses”, and “The Representation of Representations”. * exploring rewriting these posts and integrating them into a book on Meta-Science.

4) Blogging, Synthetic Daisies (15): * monthly CoE post (3 total). This includes three Fireside Science posts (cross-posts), post on DevoWorm project, and supplemental readings for the Cosmos reboot. * highlight: “The Long Game of Human Biological Variation”.

* consolidated all supplemental readings for Cosmos (13 total) into a single, printable volume (available on Academia.edu). 5) Social Media, other (1): * became an administrator for CoE on Facebook. 6) Collaborative Projects, DevoWorm: * white paper (three versions) completed, posted to Figshare (with Stephen Larson, Mark Watts, Steve McGrew, and Richard Gordon).

* Synthetic Daisies blog post on project. * datasets procured (with help from Stephen Larson and Mark Watts). Three types of data: cell lineage, gene expression, and 4-d microscopy. First two are in analyzable form and available at Github, last one is in the process of being extracted from movies and other files. 7) F1000 Neuroscience manuscript (1): * “Animal-oriented Virtual Environments: illusion, dilation, and discovery” is in development, available now as preprint at PeerJ. * send paper to Corey Bohil for review (on 5/5/2014), will be getting back to me soon (sent reminder on 6-16-2014). 8) bioRxiv and transcription/translation mRNA modeling manuscripts (2): * split up manuscript entitled “Mechanism Alteration Reveals Patterns of Cellular Information Processing” (revised and rejected at PLoS One) into two, smaller manuscripts:

* wet-lab work focused “extended protocol” submitted and accepted to bioRxiv (Using Polysome Isolation with Mechanism Alteration to Uncover Transcriptional and Translational Dynamics in Key

Genes, doi:10.1101/006213). According to bioRxiv analytics, there have been 107 views and 10 downloads in the month of June. * computational modeling focused paper submitted to 52nd Allerton Conference on Communication, Control, and Computing and bioRxiv (in progress). 9) Cancer/proliferation gene analysis for collaboration with Cellular Reprogramming Laboratory: * analysis complete, verified by Steven Suhr (limited qPCR validation). * paper not going forward due to problems with cell lines, experimental design. Next steps unclear.