Please join us for this months DISC Forum!
Guest Speaker Lenore Cowen will be speaking about her new 2022/2023 Seed Grant: "RESTORE: Building a data science and bioinformatics infrastructure for studying Coral Reef Data"
Abstract and Bio:
Title: MEDFORD: MEtaData Format for Open Reef Data
Abstract: Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space-to-store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEtaData Format for Open Reef Data (MEDFORD), in which scientists can record all details relevant to their research. Being human-readable, easily editable and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. We are initially applying MEDFORD to coral research, documenting research from RNA-seq analyses to photo collections. We are interested both in further development of the MEDFORD language (as well as helper tools that make it easier to author MEDFORD files as well as translate MEDFORD into other accepted data formats), as well as MEDFORD-enabled projects that will harness the rich multimodal data sets that are emerging around the corals domain specifically, in order to help scientists gain insight in how to save them from stressors such as pollution, disease, and climate change.
Bio:
Dr. Lenore J. Cowen is a Professor in the Computer Science Department at Tufts University She also has a courtesy appointment in the Tufts Mathematics Department and in the Tufts Graduate School for Biomedical Sciences. Her research interests span three areas: Discrete Mathematics (since high school), Algorithms (since 1991 in graduate school) and most recently Computational Molecular Biology, where she focuses on predicting protein function from structural and biological network information. She led a team that won the DREAM Disease Module Identification challenge in 2016. She is on the Editorial Board of the IEEE/ACM Transactions of Computational Biology and Bioinformatics (TCBB) and an Associate Editor of the journal Bioinformatics(from Oxford University press). In 2020, she was awarded both the CRA-E Undergraduate Research Faculty Mentoring Award from the Computing Research Association, and the NCWIT Undergraduate Research Mentoring Award from the National Center for Women and Information Technology. She currently leads the NSF funded T-Tripods Institute on interdisciplinary approaches to studying the foundations of data science.