Hi Jin, Thanks for your email. In fact, we've used OODT in the context of NCI settings as a LIMS systems for several University Hospitals, including helping to capture lung biomarker images, and then make them available in an organ-map setting. The components that you are going to want to take a look at include the filemgr, the curator, all of the metadata extractor framework, and then the workflow system.
Java development isn't required per-se to use any one of those components out of the box, but might be required if you plan on extending the components, or adapting them to run your algorithms, etc. It's not too painful though and we're here to help, so let's get started. One place you may want to start out on is the user guides for the various components, I mentioned above. You can find them here: http://oodt.apache.org/components/maven/filemgr/user/basic.html http://oodt.apache.org/components/maven/curator/user/basic.html http://oodt.apache.org/components/maven/metadata/user/basic.html http://oodt.apache.org/components/maven/workflow/user/basic.html Note, each one of these guides is available when you click the Components tab at the top of the website then pick a component from the list, then go from there and click on a guide available in the bottom right of the component specific pages. One of the important things to start thinking about: 1. What types of products/files are you guys planning to capture? 2. What metadata elements do you want to catalog/ingest? 3. How are you going to extract the metadata? a. are there existing extractors or do you need to build new ones? b. how to integrate those extractors? 4. How you want to deliver data + metadata out the other end of the catalog/archive? 1-4 should help to get going on ingestion. We'll tackle processing when you get there :) HTH for now! Cheers, Chris On Jan 11, 2011, at 9:21 PM, Jin Sung Kim wrote: > Hi, > > > > My name is Jin, and I am interested in adopting OODT as a Laboratory > Information Management System (LIMS) primarily to manage our next generation > sequencing (NGS) raw and filtered data, as well as quality control processes > in our work flow. I do see that the National Cancer Institute has utilized > OODT to manage biomarker data from various resources, which may have some > overlapping functionalities with our requirements. Do you have any > additional information regarding the use of OODT as a LIMS system that's not > available on the website, and do you foresee any difficulties that might > arise? Our team is comprised of bioinformaticians, and very few of us are > extremely familiar with Java development, though we are all somewhat > familiar with software development in general. Thank you very much. > > > > Jin > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Chris Mattmann, Ph.D. Senior Computer Scientist NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA Office: 171-266B, Mailstop: 171-246 Email: [email protected] WWW: http://sunset.usc.edu/~mattmann/ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Adjunct Assistant Professor, Computer Science Department University of Southern California, Los Angeles, CA 90089 USA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
