PPT-Homology curation at SGD:

budding yeast as a model for eukaryotic biology Stacia R Engel Stanford University Challenge to Biocurators Promote ways in which yourorganism and r esearch on yourorganism . IntAct. and . InterMine. : SGD . Rama Balakrishnan. Saccharomyces. Genome Database. Gene Ontology Consortium. Stanford University, CA. USA. Outline . Advantages of collaborating. When do you collaborate?. Multi-dimensional . Persistent Homology. Matthew L. Wright. Institute for Mathematics . and . its Applications. University of Minnesota. in collaboration with Michael . Lesnick. What is persistent homology?. Big . dATA. . & Huge Models. Alex Beutel. Based on work done with . Abhimanu. Kumar, . Vagelis. . Papalexakis. , . Partha. . Talukdar. , . Qirong. Ho, Christos . Faloutsos. , and Eric Xing. Big Learning Challenges. Open Repositories 2012. Stacy Kowalczyk. Beth . Plale. Kavitha Chandrasekar. Yiming Sun. Agenda . Introduction to Digital Curation. Workflow Systems Overview. Workflows for Digital Curation. Break. Implementing Workflows in Trident . Yusu. . Wang. Ohio State University. AMS Short Course 2014. Introduction. Much recent developments in computational topology. Both in theory and in their applications. E.g. , the theory of persistence homology. A Plan for Curation Services: . Organization, Technologies, Communities. The Original NDIIPP Partners: . Plans for Moving Forward. Patricia Cruse, Director, UC3, CDL. The current landscape. Ever increasing number, size, and diversity of content. Benjamin J. . Liebeskind. Post-doctoral Fellow, UT Austin. PIs: Edward . Marcotte. , Rick Aldrich. How do we compare proteins across species?. Gravitropism defects. Waardenburg. syndrome. Significantly . Sept 4, 2013. Clustering Via Persistent Homology. Creating a simplicial complex. Step 0.) Start by adding 0-dimensional vertices . (0-simplices). Creating a simplicial complex. 1. .) . A. dding . 1. http://evolution.berkeley.edu/evolibrary/article/0_0_0/similarity_hs_01. Inherited Traits. People . look like one another for different reasons. Two sisters, for example, might look alike because they both inherited . SGD overview. Accessing data. Finding . S. . cerevisiae. . homologs. Fungal genomes to BLAST. Saccharomyces . Candida. Saccharomycetaceae. Other . S. accharomycetales. (budding yeasts; ex: . Pichia. Comparative study of . morphological and anatomical structures. of animals and plants also indicate that they are constructed on the same basic plan and they shows certain similarities.. Such similarities are observed in:. hm bghkcgnnc, nesdm hm sgd ehrrs 01 lnmsgr ne khed- Hs hr rdonrsdc sn aeedbs 00–10% ne bghkcrdm- Dbydla hr arrnbhasdc vhsg nsgdr asnohb bnmchshnmr hmbktchmf arsgla amc gaxedudr- Eabsnrr sgas bnm gdacabgd- Sgd gdacabgdr nbbto nudo 04 shldr a lnmsg eno as idars a lnmsg as a shld, amc sgd ctoashnm ne dabg assabk uaohdr eonl aants 04 lhmtsdr sn ailnrs sgodd gntor- Sgdod aod mn boamhai atsnmnl Prove It!. Biogeography. Homologous and Analogous Structures. Fossil record. biogeography. The geographic distribution of plants and animals over the surface of the Earth. Pangaea. 270 million years ago all of the planet’s land mass was combined into one super continent.