An introduction to git & GitHub: The standard tools for version control

Alex de Siqueira is a postdoctoral researcher at BIDS, working on open source algorithms for processing computed tomography (CT) 3D images. He received his MS and PhD from the State University of São Paulo, Brazil, applying image processing tools to tackle challenges in materials science and geochronology. A core developer of scikit-image, he is an open source and free software enthusiast since his first contact with Linux, in 2000, contributing to several projects and events in Latin America and Europe. Alex also worked as a postdoctoral fellow at the State University of Campinas, Brazil, and the TU Bergakademie Freiberg, Germany, where he created pytracks and wrote Octave - Your first steps on scientific programming (in Brazilian Portuguese).

BIDS Biology and Environmental Sciences Lead Ciera Martinez focuses on data intensive research projects that aim to understand how life on this planet evolves in reaction to the environment and climate – especially projects involving large and complex datasets.  A long-time open science advocate, Ciera has been involved with and continues to be interested in working on training for open data, education, publishing, and software, including developing community standards for data management practices.  As a 2019 Mozilla Open Science Fellow, she connected her love of data and museums and worked on projects aimed at understanding and increasing the usability of biodiversity and natural history museum data.  She received her PhD in Plant Biology from UC Davis, researching the genetic mechanisms regulating plant architecture.  She then went on to become a NSF Postdoctoral Fellow at UC Berkeley in the Molecular and Cellular Biology Department, studying genome evolution.  She was also a BIDS postdoctoral Data Science Fellow for 3 years, working on undergraduate research practices, data science training, community development, and best practices for data science, diversity and inclusion, and computational research.  

Adam G. Anderson advised graduate students in the Computational Social Science Training Program, managed the Computational Social Science Forum, and helped organize BIDS's cross-domain (XD) initiatives.  He was also a lecturer in Digital Humanities and Data Science, and an academic coordinator for Digital Humanities at Berkeley, where he co-authored and designed the Theory and Methods curriculum for the DigHum Minor and Certificate Program. He was also a co-coordinator for the Digital Humanities Working Group (DHWG) and the Computational Text Analysis Working Group (CTAWG), as well as the topic area lead in Network Analysis and Text Analysis at the D-Lab.  His work brings together the fields of computational linguistics, archaeology and Assyriology / Sumerology to quantify the social and economic landscapes emerging during the Bronze Age in the ancient Near East.  His research interests include network analysis, archival studies, geospatial mapping and language modeling (NLP).  He applies these mixed methods to large datasets of ancient texts and archaeological records, in order to better understand the lives of individuals and groups within ancient societies, and to relate these findings within the context of our lives today.  He holds a PhD in Near Eastern Languages and Civilizations from Harvard University, an MA (zwischenprüfung) in Assyriology from  Ludwig-Maximilians University, and a BA in Linguistics from Brigham Young University.

Maryam Vareth leads BIDS’ data science research efforts in the Health & Life Sciences.  Dr. Vareth is a Co-Director of the Innovate For Health initiative, a collaboration among UC Berkeley, UCSF, and Janssen Pharmaceutical Companies of Johnson & Johnson. As an experienced engineer, researcher, and data scientist, she applies mathematics, statistics and physics to solve unmet needs in healthcare to enhance patients’ experience during their medical journey. She is an advocate for “data-driven” medicine, and in particular for linking medical imaging data with medical diagnostics and therapeutics to extract clinically-relevant insights through the use of open research and open source practices.  Dr. Vareth received her BS and MS training in Electrical Engineering and Computer Science (EECS) from UC Berkeley, where she was awarded the prestigious Regent’s and Chancellor’s Scholarship.  She completed her PhD through the joint UC Berkeley-UCSF Bioengineering program as a National Science Foundation Fellow, where she was awarded the Margaret Hart Surbeck Endowed Fellowship for Interdisciplinary Research for her work on developing new techniques and algorithms for the acquisition, reconstruction and quantitative analysis of Magnetic Resonance Spectroscopy Imaging (MRSI), with the goal of improving its speed, sensitivity and specificity to improve the management of patients with brain tumors.  She conducted her post-doctoral fellowship at UCSF, combining structural, physiological and metabolic imaging data from large clinical trials to quantitatively characterize heterogeneity within malignant brain tumors.

Marsha Fenner is the Communications/Program Manager for the Berkeley Institute for Data Science. In this role, she works to connect researchers and data science practitioners across a wide array of academic disciplines, facilitate interdisciplinary collaboration, and implement training and education programs that engage and expand BIDS' and Berkeley’s active and diverse research community. Fenner has managed communications, training/education/outreach programs, and administrative operations for scientific programs and research initiatives at UC Berkeley and Lawrence Berkeley National Laboratory, including the Innovative Genomics Institute, the DOE Joint Genome Institute, and Berkeley Lab's Advanced Light Source. She holds an MA in philosophy and comparative religious studies, and a BA in classics, philosophy and mathematics.

David Mongeau, now the Founding Director of the School of Data Science at the University of Texas at San Antonio, was the Executive Director of BIDS from April 2018 to June 2021. During that time, in collaboration with the Faculty Director and Faculty Council, he set strategic direction and oversaw the BIDS research, training, and outreach. He also led the institute’s industry and foundation relations and its engagement with other UC and global research institutes, all toward the overarching mission at BIDS to create and deploy data science methods, practices, and technologies to enable discovery. Previously, David co-led the data analytics institute at Ohio State; worked at Battelle, where he championed its proposal for an AI and cybersecurity company, now Covail; and worked for many years at Bell Labs – starting on the team that introduced the first C++ compiler and UNIX System V and leaving after building a global business and technology consulting practice, now part of Nokia Bell Labs Consulting. David earned his undergraduate degree at Carnegie Mellon University, and later earned a graduate degree at Rensselaer Polytechnic Institute and an MBA from Purdue University. Many of his interests lie beyond data science, embracing the humanities and arts.