Course: Reproducibility for Biomedical Researchers - 2019 | UCSF-CLE

  • Instructor: Ariel Deardorff - UCSF Library Data Science Initiative

    Panelists:

    • Stephen Floor, PhD - UCSF 
    • Byron Smith, PhD - Gladstone
    • Seemay Chou, PhD - UCSF
    • Perrine Janiaud, PhD - Stanford 


    Overview

    Join us as we launch the fall Workshop series on Reproducibility for Biomedical Researchers! This session will start with an overview of the reproducibility "crisis" and highlight solutions for making research more reproducible. We will then hear from a panel of UCSF and Bay Area researchers about how they work to improve reproducibility in their work. Finally, we will conclude with a reception giving you a chance to connect with UCSF colleagues over food and drink

    Learning Objectives

    By the end of this session, learners will be able to:

    • Define reproducibility in the context of the biomedical sciences
    • Describe two causes of non-reproducible research
    • Identify one practice or tool to improve the reproducibility of their work

    Instructor Bio

    Ariel Deardorff is the UCSF Data Services Librarian and member of the Library’s Data Science Team. She teaches classes and does research on data management, open science, and reproducibility in the health sciences. She has a Master’s degree from the University of British Columbia and was a National Library of Medicine Associate Fellow before arriving at UCSF.

    Course Materials

    Topic
    1

  • Instructor: Karla Lindquist, PhD - UCSF Library Data Science Initiative

    Overview

    The scientific community, and many publishers, are increasingly demanding that experimental results be reproducible in order to be considered valid and valuable contributions. In order to achieve this, researchers must design their experiments carefully. In this workshop, we will review some of the key steps to consider in these critical planning stages.    

    Learning Objectives

    By the end of this workshop, learners will

    • Be aware of different types of experimental biases
    • Know what to consider in developing a good analysis plan
    • Be able to identify the key components of a well-written methods section

    Instructor Bio

    Karla teaches and consults on topics related to statistics and bioinformatics, as well as programming in R. She also has expertise with shell scripting and other languages.

    Course Materials


    Topic
    2

  • Instructors: Veronique Kiermer and Dan Morgan - PLOS

    Overview

    Scholarly communication is steadily moving towards an open environment through open access publishing, self-archiving, and increased transparency around the work that goes into scholarly research outputs. Learn about new forms of publishing such as micropublications, null and data results, registered research reports and preprints, and how tools like ORCID and social media can help shape and promote your online scholarly identity. 

    Learning Objectives

    By the end of this workshop, learners will be able to

    • Define the economics of scholarly publishing and the hurdles to publishing open access
    • Explain how emerging models of scholarly communication improve reproducibility
    • Describe the best ways forward to an open research communication system
    • Identify scholarly communication tools to help manage their online presence

    Instructor Bios

    Veronique Kiermer joined the publisher PLOS in 2015 as Executive Editor, responsible for editorial and content direction and vision for the PLOS suite of journals. Prior to PLOS, Veronique was Director of Author and Reviewer Services for Nature Publishing Group (NPG) where she oversaw the Nature journals research integrity and editorial policies. She also focused on the author and reviewer experience across the publishing portfolio of NPG. Veronique was the founding Chief Editor of Nature Methods and subsequently took on publishing responsibility for the title and other online products. In 2010 she became Executive Editor, NPG, overseeing editorial policies and editorial quality assurance for Nature and the Nature journals. Veronique obtained her PhD in molecular biology from the Université Libre de Bruxelles, Belgium and completed postdoctoral work at UCSF. 

    Dan Morgan is the Director of Community Relations at PLOS, where he guides PLOS' strategic engagmenet with core scholarly publishing and research communities. Prior to his position at PLOS, Dan led the launch of the new, value-sharing, open access journal Collabra at UC Press. He also worked as Senior Manager of Global Academic Relations, Executive Publisher, Publishing Editor, and Editorial Assistant with the publisher Elsevier. His core skills are in journals/product management and launch, communications, product strategy, market analysis, scientometrics, altmetrics, community-building, advocacy, open access and open science.

    Course Materials

    Topic
    3

  • Instructor: Lenny Teytelman, PhD - Protocols.io

    Overview

    One of the barriers to reproducibility of research is the lack of detailed methods in published articles and in the lab environment. Open sharing of research protocols improves replication by making research processes accessible, dynamic, and open to discussion, modification, and optimization. Learn how protocol sharing meets openness and transparency guidelines such as TOP (Transparency and Openness Promotion). 

    Learning Objectives

    By the end of this workshop, learners will be able to:

    • Define the benefits of making research protocols open
    • Prepare, share, and modify a research protocol
    • Identify guidelines and best practices for research methods and protocols

    Instructor Bio

    Lenny has over a decade of computational and experimental biology experience. He did his graduate studies at UC Berkeley, and it was his struggle with correcting a published research method as a postdoc at MIT that led him to cofound protocols.io. Lenny brings to protocols.io a strong passion for open access, sharing knowledge, and improving research efficiency through technology.

    Course Materials

    Link to class slides on Google

    Topic
    4

  • Instructor: Karthik Ram, PhD - Berkeley Institute for Data Science

    Overview

    Most modern advances in science have been made possible thanks to use of software. This software, also known as “research software”, has become essential to progress in science and engineering. Data and publications most often created, analyzed, and stored electronically, using tools and methods expressed in software. Despite the importance of research software for science, a majority of scientists do not have sufficient training and understanding of best practices that allow for reuse and reproducibility of software artifacts. 

    In this workshop you will learn how to set up you work so others can easily reproduce all of your computational steps and generate outputs in a variety of formats. You’ll also learn about best practices for sharing code, when to turn a loose collection of scripts into a software package, and how to get academic credit for such work.

    Learning Objectives

    By the end of this session, participants will be able to:

    • Explain several ways in which to share their work as reproducible notebooks.
    • Share and archive code/software associated with papers

    Instructor Bio

    Karthik is a senior research data scientist at the Berkeley Institute of Data Science and a co-founder and director of the rOpenSci project, and The US Research Software Sustainability Institute. Karthik is also a senior PI at the UC Berkeley Initiative for Global Change Biology. Prior to joining Berkeley, he earned his PhD in Ecology & Evolution from the University of California, Davis. Much of his recent work focuses on building tools and services around open data and growing diverse data science communities.

    Course Materials

    Slides and resources from this workshop are available on GitHub

    Topic
    5

  • Instructor: Jessica Polka, PhD - ASAP Bio

    Overview

    Peer review is an essential mechanism for validating research results. This workshop will examine the function of peer review, its shortcomings, and efforts to make peer review more transparent, inclusive, and unbiased. Learn about peer review training opportunities and recognition for review work.

    Learning Objectives

    By the end of this workshop, participants will be able to:

    • Name emerging peer review models
    • Get credit for peer reviewing
    • Provide feedback on a publicly posted preprint

    Instructor Bio

    Jessica Polka serves as Executive Director of ASAPbio, a researcher-driven nonprofit organization working to promote innovation and transparency in life sciences publishing in areas such as preprinting and open peer review. Prior to this, she performed postdoctoral research in the department of Systems Biology at Harvard Medical School following a PhD in Biochemistry & Cell Biology from UCSF. Jessica is also a Plan S Ambassador, a research affiliate at MIT Libraries, a steering committee member of Rescuing Biomedical Research, and a member of ASCB’s public policy committee. Formerly, she was president of the board of the nonprofit Future of Research and a member of the NASEM Next Generation Researchers Initiative.

    Course Materials

    Link to class slides on Google 

    Topic
    6

  • Instructor: Daniella Lowenberg - California Digital Library

    Overview

    Research data is increasingly valued as a necessary component of reproducible and open science. Initiatives focused on the usability of data like “FAIR”, coupled with mandates from funders and publishers that require data to be openly accessible, increase the need for a data savvy research workforce. This workshop will focus on understanding the value and need to publish research data and how and where to publish data in a usable way that allows for reproducibility and transparency that advances scientific discovery.

    Learning Objectives

    By the end of this workshop, learners should be able to

    • Describe the value and need to publish research data openly
    • Utilize UCSF (and global) data publishing resource: Dryad

    Instructor Bio

    Daniella has a background in Microbiology. After leaving the lab, she was a Publications Manager at PLOS ONE where she implemented and oversaw the PLOS Data Policy. For the last three years, Daniella has been a data publishing and data metrics product manager at California Digital Library, within the University of California, focusing on cross-organizational and global efforts in open research data practices. She is currently the Product Manager for Dryad and project lead for the Sloan Foundation funded Make Data Count initiative.

    Course Materials

    Topic
    7

  • Instructor: Elizabeth Silva, PhD - UCSF Graduate Division

    Overview

    Aspects of the culture of academic research can be at odds with efforts to improve rigor and reproducibility, from hyper competition for jobs, funding and fame, to the everyday devaluing of “administrative tasks” as a part of scientific practice. In this workshop, participants will explore the cultural barriers to implementing rigorous and reproducible practice.

    Learning Objectives

    By the end of the session, participants will be able to:

    • Describe the broad cultural barriers to rigor and reproducibility
    • Identify at least one cultural barrier that is impeding their own practice in rigor and reproducibility
    • Develop a strategy to implement in everyday practice for improvement of rigor and reproducibility

    Instructor Bio

    Liz is a trained biomedical research scientist with interests and experience in science policy, particularly relating to publication and research ethics, reproducibility of research, and training of biomedical graduate students and postdocs.

    After completing her PhD and postdoctoral training in developmental biology and genetics (in Canada, the UK and the US), she moved to PLOS ONE as an Associate and then Senior Editor. She returned to UCSF in 2014 where she managed the Motivating INformed Decisions (MIND) program, one of 17 experimental programs across the country that aimed to bring biomedical research training in line with the realities of the career outcomes for graduate students and postdocs. In 2016 she became the Associate Dean for Graduate Programs in UCSF's Graduate Division.

    She has served as a panelist and speaker on a variety of topics in science policy, including: reproducibility in research, ethical conduct in research and publishing, research communication and publishing for scientists, career exploration and professional development for PhDs, and issues related to the roles of PhD trainees in the biomedical workforce and in academia. 

    Course Materials


    Topic
    8