Woo hoo! Kudos to my colleague Sungwon Jung and the team for getting a paper accepted to WSCB 2011 this summer!
Jung S., Verdicchio M. P., Kiefer, J., Berens, M., and Kim, S. (2011) “Learning Contextual Gene Set Interaction Networks of Glioblastoma and Identifying Subtype Specificity.” In Eigth International Workshop on Computational Systems Biology (WCSB 2011), June 6-8, 2011, Zurich, Switzerland (to appear).
It’s been a while but I’ve updated most of the site, including my research page, publications, teaching comments, and even a picture of my face!
I’ll be teaching again this spring — CSE 182: Applied Problem Solving with C# .Net. If you are a future student finding this post because you are going all Internet Detective on me, nice to meet you. I look forward to meeting all you in a few weeks, and to making the semester productive and interesting.
This was really insightful. I’m working on a major change in how I tackle my days, and this article has a lot of great advice from a fellow grad student!
I’ll be teaching CSE 110 Principles of Programming with Java this fall 2010 semester at ASU. The section line number for the lecture is 71670. If you are finding this post because you are a student doing a Google search on me, hello. I’m looking forward to teaching this semester, and you can check out some comments from previous students on the right. See you in August!
I spent a while trying to figure this out and almost emailed developers, but then I found this simple solution. Some projects you want to work on use Ant build files, but you (I) use Eclipse. Their documentation says to download Ant and do it command-line style, but that’s a pain especially because you (I) know Eclipse has ANT built in. So you right-click the build.xml file and try to run Ant, but it says that it can’t find a compiler or that JAVA_HOME points to your JRE (instead of JDK). According to this website:
http://www.practicalembeddedjava.com/tools/eclipse_tips.html
Eclipse/Ant doesn’t use your system variables to find anything, so all you have to do is add tools.jar to Window>Preferences>Ant>Runtime>Classpath>Ant Home Entries with “Add External Jars”. Since the screen shot at the site above is a little dated, I made one with my newish version of Eclipse (below). Now the Ant build went fine (clean the project if you have to), and now you can run projects depending on Ant from Eclipse.
(click the image a couple times to see the big version)
I’ve still been working, but just not updating this a lot. Currently I am working on improving Bayesian network learning for gene regulatory network applications as well as generating synthetic data containing a mixture of cellular contexts (see the context mining page). Such data will allow us to do some quantifiable analysis of the performance of context-specific network inference techniques since we’re relying only on empirical studies at the moment. Also on the table is further study of identifying context-specific regulatory behavior, causal network inference techniques, and work on the aging project. Classes start again in a few weeks and I’ll be taking data mining and perhaps a reading group on biomolecular networks.
Sometime during ROCKY ’08 I’ll be presenting the current status of the Causality work I’ve taken over from Xin Zhang. It’s in Aspen, CO and all the details are on the Causal Networks page.
Information has been added to the pages for my three main research projects: Cellular Context Mining, Causality, and Aging. Feel free to check them out and comment.
My group’s manuscript, “Context-Specific Gene Regulations in Cancer Gene Expression Data,” was accepted to the 2009 Pacific Symposium on Biocomputing (link). I’ve posted the manuscript on the Research page.
