josiah tree
Present
I'm a MS/PhD research student in the Energy and Resources Group at UC Berkeley, and will get my MS in 2009. My broad interest is promoting peaceful communities through sustainable development and appropriate technologies.
Research Projects
  • 2008 to present. SWITCH: Optimizing clean energy investments for large electric grids.
  • 2008 to 2009. Rural Electrification Guide: Documentation of how to locally manufacture and deploy small wind turbines for rural electrification.
  • 2008. Cost of Avoided Carbon: Cataloguing the potential and costs of various strategies for reducing carbon emissions.
Biography
I grew up outside of St.Paul, a small town in Northwest Arkansas. In 1998, I graduated from the Arkansas School for Mathematics and Sciences. In 2002, I graduated from the University of Arkansas, Fayetteville, with a B.S. in Computer Science and a minor in math, and eight months experience in advocating for peace. I then spent six months digging ditches, working with a master stone mason, touring the mid-south on a 1976 Honda CB 540, and waiting for employment paperwork for a research position in the National Institute on Aging. I spent the next four and a half years in Baltimore working in the Image Informatics and Computational Biology Unit, developing portions of the Open Microscopy Environment (an Open Source image database and analysis system for scientific and medical applications), and developing pattern recognition tools for muscle aging studies. In my off-time I advocated for peace and social justice in respect to international debt and trade agreements, as well as serving on the board of the Greenmount West Community Development Corporation. For fun, I enjoy brainstorming, hiking, biking, reading, playing, conversing, building furniture, making art, and collecting stories. In 2007, I quit my job at the NIA to pursue graduate studies at UC Berkeley.
Publications
  1. Johnston, J.L., Iser, W.B., Chow, D.K., Goldberg, I.G., Wolkow, C.A. (2008 ) Quantitative Image Analysis Reveals Distinct Structural Transitions During Aging in Caenorhabditis elegans Tissues. PLOS One. 3:7. Available online.
  2. A. M. B. Tadeu, S. Ribeiro, J. Johnston, I. Goldberg, D. Gerloff, W. C. Earnshaw (2008). CENP-V is required for centromere organization, chromosome alignment and cytokinesis. EMBO J. 27, 2510-2522. Available online.
  3. N. Orlov, L. Shamir, T. Macura, J. Johnston, D. M. Eckley, and I. G. Goldberg, (2008) WND-CHARM: Multi-purpose image classification using compound image transforms, Pattern Recognition Letters. 29:11-1684. (pdf)
  4. Shamir, L., Orlov, N., Eckley, D. M., Macura, T., Johnston, J., Goldberg, I., (2008) Wndchrm - An Open Source Utility for Biological Image Analysis. BMC - Source Code for Biology and Medicine. 3:13. Available online.
  5. Chow, D.K., Glenn, C.F., Johnston, J.L., Goldberg, I.G., and Wolkow, C.A. (2006) Sarcopenia in the Caenorhabditis elegans pharynx correlates with muscle contraction rate over lifespan. Exp. Gerontol. 41:252-60. (pdf)
  6. Johnston, J., Nagaraja, A., Hochheiser, H., and Goldberg G. (2006). A Flexible Framework for Web Interfaces to Image Databases: Supporting User-Defined Ontologies and Links to External Databases. 2006 IEEE International Symposium on Biomedical Imaging. (pdf)
  7. Orlov, N., Johnston, J., Macura, T., Wolkow, C., Goldberg, I. (2006) Pattern Recognition Approaches to Compute Image Similarities: Application to Age Related Morphological Change. 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano. p1152 - 1155. (pdf)
  8. Goldberg, I., C. Allan, J.-M. Burel, D. Creager, A. Falconi, H. Hochheiser, J. Johnston, J. Mellen, P.K. Sorger, and J.R. Swedlow. (2005). The Open Microscopy Environment (OME) Data Model and XML File: Open Tools for Informatics and Quantitative Analysis in Biological Imaging. Genome Biol. 6:R47. (pdf)
Book Chapters
Conferences
  1. Kantner, J.W., Hoffman, I.M., Johnston, J.L., Levin, J.E., Komiyama, R., Motschenbacher, A., Fripp, M., Gimon, E., Kammen, D.M.; The Cost of Conserved Carbon (C3): A Modeling System for Evaluating the Monetary, Social, and Carbon Implications of Regional-, National-, and Global-Scale Energy Choices. American Geophysical Union 2008 Join Assembly. Fort Lauderdale, FL. 2008.
  2. Macura, T., Johnston, J., Cordero, J., Orlov, N., Shamir, L., and Goldberg, I. G. Quantitative pattern analysis of a large tissue collection across multiple experimental variables. Proc. Workshop on Bio-Image Informatics, October 2007.
  3. Cordero, J., Macura, T., Johnston, J., Goldberg, I. G., Quantitative Morphometry of Mouse Tissue during Aging. Presented at the 2007 Annual Biomedical Research Conference for Minority Students.
  4. Goldberg, I., David, L., Hochheiser, H., Johnston, J., Orlov, N., Creager, D., Hughes, B., Mellen, J., Burel, J-M., Allan, C., Falconi, A., Brauner, E., Sorger, P., and Swedlow, J. OME: Image Informatics in a Post-Genomic World. American Society for Cell Biology, 2003 Annual Meeting, December 2003.