Week 9 : Reproducibility of Script-Based Workflows – Wrap up

For this week, I kept working on reproducing the LIGO script on docker and Reprozip experiment by building “LIGO script” container on top existing YW container.  Additionally, I tried to understand the bridge between Docker and Reprozip which are for sharing dependencies but orthogonal kinds docker, i.e one is for software dependencies; Continue reading Week 9 : Reproducibility of Script-Based Workflows – Wrap up

Week 5: New/Emerging Communities

This week’s activities: Sent out first round recruitment to a list of people in Synthesis Centers. Contacted Amber for more potential participants. Expanded the list of case studies. Looked at member nodes such as USGS, NEON, KNB, LTER, etc. Updated bibliography with a series of papers on interdisciplinary collaboration. Next Continue reading Week 5: New/Emerging Communities

Week 9: Documentation and finishing up with evaluation

Since the past few weeks, I was working on evaluating the ontology matching algorithm on our dataset. After completing the code for performing evaluation and running it, 0 values for precision, recall and f-score were obtained. Manual inspection of the source ontologies revealed that  the “class name” were uninformative and Continue reading Week 9: Documentation and finishing up with evaluation

Week 8 : Reproducibility of Script-Based Workflows – Docker and ReproZip experiment

After a week concentrating on reproducing the LIGO script on docker and ReproZip experiment, I encountered some issues with “broke” data dependencies and software dependencies when running script on different platforms, but finally figured out how to solve them.I also made document about reproducibility in light of the system dependencies issues for deployment Continue reading Week 8 : Reproducibility of Script-Based Workflows – Docker and ReproZip experiment

Week 8: Optimizing ontology matching algorithm

This week, I continued with the evaluation task that I was working on last week. Since the ontology matching algorithm was extremely slow, I looked into the AgreementMaker Lite (AML) tool to identify the main cause. I found out that the algorithm loads in the source and target ontologies in several Continue reading Week 8: Optimizing ontology matching algorithm

Week 9: Evaluate Instrument for Education – Final Week

     As I am wrapping up the last week of the internship project with my mentors, I would like to take this opportunity to first thank my mentors, Amber Budden and Heather Soyka of DataONE and Viv Hutchison of U.S. Geological Survey for all of their help and guidance Continue reading Week 9: Evaluate Instrument for Education – Final Week