Geoffrey Lovelace is a black-hole physicist and he and his students simulate with high-performance computing (HPC) all things space-time around colliding black holes, especially as a source of gravitational waves.
Biology summer interns Christina Chavez and Richard Leyba bring their high-performance computing to GWPAC
Joshua Der is a plant biologist specializing in evolutionary genomics, focusing on ferns and parasitic plants. Besides the research in his new wet lab across from GWPAC, he and his students use HPC to sort through extremely large genetic data sets to reconstruct the deep evolutionary history of plants.
The routine mechanics of HPC and cluster-computer control are remarkably independent of detailed applications, and so Christina and Richard have been working alongside summer research students across GWPAC, especially Haroon Khan and Alyssa Garcia. Thus, Geoffrey and Joshua are looking to submit a joint NSF-MRI proposal, possibly with other CSUF faculty in Economics and in Computer Science, to expand computing resources within GWPAC and the college’s Center for Computational and Applied Mathematics CCAM.
Christina is currently a student at Santiago Canyon College pursuing a degree in Biology with plans to transfer to CSUF. With Professor Der, she is working on the assembly and annotation of the chloroplast genome of Santalum paniculatum, a parasitic plant native to Hawaii. These plants rely on their hosts to provide both water and nutrients and have a reduced capacity for photosynthesis. Because of this, their chloroplast genome may evolve under relaxed natural selection and can vary widely in size and gene content, greatly complicating her work. Christina is becoming adept with Unix and Linux running on the CCAM cluster and using software like Velvet and MITObim to assemble the genome. She is also learning to use the programs Dogma and Geneious to annotate the genome as well as programing in Python to help sort through their very large data sets.
Richard is a CSUF Biology major. With Professor Der, Richard is currently annotating the chloroplast DNA of Azolla filiculoides which has already been assembled as part of the Azolla Genome Project. Azolla is a genus of some seven ferns unique to the plant world with a long list of remarkable properties including being a food source and an efficient heavy metal filter. Azolla DNA has been expressed in raw data fragments, and Richard has been working to compile the resulting huge amount of information with text editing and HPC to generate the coherent and very long genome sequence. Once created, Richard will turn to the task of comparing protein sequences in Azolla with similar sequences from other ferns. In the end, he hopes to obtain a visual representation of the chloroplast genome.