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

Week 7 : Reproducibility of Script-Based Workflows project

For this week, I still worked on modifying LCA queries and started creating a Docker for the LIGO script. The main task is to make sure the container could contain YW, NW, as well as the capability to query across them using the bridge prototype, and ReproZip, then tried to answer Continue reading Week 7 : Reproducibility of Script-Based Workflows project

Week 8: Evaluate Instrument for Education – Paper, Poster, and DataONE Users Group Meeting

Continuing the work that I had started with the poster from last week, I was able to complete my first revision of the poster before my weekly meeting with my mentors. Consequently, during this week’s meeting, I was able to review the project paper, its accompanying abstract, and the poster Continue reading Week 8: Evaluate Instrument for Education – Paper, Poster, and DataONE Users Group Meeting

Week 7: Continuation of evaluation task

Last week I was able to combine several ontologies into a single owl file and load them into AgreementMaker Light. This week, I continued to work on evaluation. Following are the specific tasks I focused on: 1. For evaluation, we need to compare the matches obtained from our algorithm with Continue reading Week 7: Continuation of evaluation task

Week 3: New/Emerging Communities- Case studies

The main tasks within this week are reading papers and looking for case studies. I looked through some cases of environmental health studies and documented the environmental data used. Most of the studies in the last five years have documented their data sources very clearly and most of the data Continue reading Week 3: New/Emerging Communities- Case studies