Developer Stories

Developer Stories

By Vanessa SochatTechnology
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Developer Stories episodes

  • R for Reproducibility

    Anna Krystalli’s career took a number of interesting turns. It all started in macro biology, where Anna helped analyse data from one of the longest running ecological surveys: the Continuous Plankton Recorder Survey. Munching all the data took her into the exciting world of R programming. There she started to play an increasingly important role in the R community. This included taking on the role of associate editor of rOpenSci. Anna is passionate about making software more open, accessible and reproducible. As one of the RSE Fellows she has been instrumental in initiatives like the ReproHack. And if you ever happen to be in Sheffield, enjoy the great music scene and - climbing.

    Interesting Links
    • Sir Alistair Hardy
    • R Keynote at useR 2020 by Dr Noam Ross
    • rOpenSci
    • rOpenSci Dev guide
    • ReproHack HQ
    • Scienceverse
    • SSI Fellowship
    • Macroecological and macroevolutionary patterns emerge in the universe of GNU/Linux operating systems
    • Reinventing Discovery: The New Era of Networked Science
      • 26 min
    • The Wisdom of the Systems Engineer

      Only a few minutes into our convsersation, I knew that Bruce Wilson, a research

      systems engineer at Oak Ridge National Lab, had rich life experiences and both
      wisdom and depth from them. In our 33rd episode of Research Software Engineer Stories,
      we talk with Bruce not only about trends in systems engineering, but also empathy for self
      and others, team dynamics, diversity, and mental health. Bruce shares his story of
      shifting roles, and how solving challenges with domain scientists has brought him joy.

      25 min
    • Publish Without Perish

      The principle format of science communication - the research article - hasn’t changed for a very long time. But research as well as the processing and communication of data have all changed dramatically. Therefore, is the traditional way of publishing still the best way to share scientific results and discoveries?

      This is a question Emmy Tsang is focusing on at eLife Sciences, a non-profit organisation created by funders and researchers.

      Following her Ph.D. years in neuroscience, Emmy decided it is time to bring some badly needed change to science and research communication. With so much research based on software and with modern technologies we have available today, we should be able to make science and the sharing of results fairer, more open and faster.

      So, what will the future of scientific communication be? Will it be something like the executable research article? Will research articles be replaced with publishing individual ‘units of research’, e.g. methodologies, results etc.? Whatever the outcome, research software will play a central part in it. And, as Emmy says, change will only happen if we work together as a community.

      If you have ideas and suggestions Emmy would like you to get in touch via @eLifeInnovation or email.

      Some of the links mentioned in this episode:

      • stencila using open source tools to author and share executable documents
      • Code Check by Stephen Eglen and Daniel Nüst to have your research code checked independently
      • Binder which helps to turn Jupyter notebook repositories into executable environments
      • Hypergraph share your research as you go
      • Real Time collaboration with JupyterLab
      • Africa arXiv
      • Goolge Search why leaving your search for papers to Google may not be a good idea
        • 28 min
      • The Code Curious Biologist

        Blake Joyce asserts that he’s stumbled into his current role as assistant

        director of research computing at the University of Arizona by way of dumb luck -
        and while there might be some luck in the mix, if you listen to his story, an
        overarching theme is that Blake was not afraid to try new things, and take some
        risks. In this episode of RSE Stories, we cover a broad range of ideas from
        growing crops in the future, to what Blake sees as the next frontier,
        to how to run an effective research computing team.
        Hint - you need more than just compute. Here are some things that Blake
        is excited about:

        The Future

        He mentions computing efficiency, and here’s a list of things he is excited about:

        • Distributed data protocols like dat and IPFS
        • Benchmarking and profiling to make code “run more better” on systems. Things like this are pretty eye opening
        • Building communities to support interactions between researchers-research software engineers-cyberinfrastructure professionals like Research Bazaar and SWEETER
          • Projects He Invites you to check out!

          These projects didn’t make it into the final recording, but we want to share them here anyway. Alec Scott is the research software engineer that Blake mentioned, and he’s working on two projects that might be of interest. They’re early days still, but looking to get deployed this year:

          1. Autamus - An autonomous containerized build system
          2. Arken - A distributed data archiving system
            3. 21 min
          3. How to make beer better

            For this episode our journey through RSE land takes us to Belgium. James Collier and Alexander Botzki work at the Flemish Institute for Biotechnology (Vlaams Instituut voor Biotechnologie - VIB). Belgium being famous (amongst many other things) for its beers, lovers of the beverage will appreciate the work James and Alexander do to improve its taste using software technologies such as machine learning.

            Equally important to their work is community building. They are deeply involved with the Elixir project, a pan-European network for life sciences. Realizing the importance of software engineering in research, they recently set up an RSE association for Belgium. Alex and James are excited to announce their first Research Software Developers Day on 3 Dec 2020.

            Other Interesting Links
            • Belgian Beer App from Supinya Piampongsant at the Kevin Verstrepen lab (data collection, experiments, AI). VIB Bioinformatics Core provided the web-site.
            • Flemish Gut Flora: at the Jeroen Raes Lab.
              • 21 min
            • Science Gateways

              Sandra Gesing is a powerful force in the world of research software engineering.

              In fact, she spans the worlds of high performance computing, professorship,
              computer science, and having a leadership role in the United States Research Software
              Engineering Association. In this episode, Sandra shares her background from the start
              of being captured by answering scientific questions, to discussion of the importance
              of scientific gateways. Are you planning your post COVID trip to Chicago or
              places in Europe? Sandra has some suggestions for you!

              26 min
            • Opening Eyes and Turning Lights On

              Today we meet with Radovan Bast (@__radovan, Homepage) from Tromsø in Northern Norway. Radovan moved into software engineering via theoretical chemistry. The journey wasn’t easy, or as Radovan put it “I had imposter syndrome.” However, one of the highlights in this transition has been teaching others software and watch “eyes opening and lights turning on.” In our session we talk about some of Radovan’s exciting projects like Cicero - shared presentations or filtering and finding misinformation. He is also co-author of the CMake Cookbook.

              Radovan is closely working with colleagues in Norway, Sweden, Finland and other countries to build and grow a Nordic RSE organisation, kicking off with a conference planned for December 2020 in Stockholm (Covid-19 permitting).

              38 min
            • A Lifelong Learner

              This week on RSE Stories, we take a blast into the Python Universe! Our guest

              Carol Willing is not only a core developer for CPython, Jupyter Hub, and mybinder.org,
              she is an overall leader in the Python community with much wisdom about how to
              be a lifelong learner, and find passion in your work. What’s the difference
              between IPython and Jupyter? Take a listen to find out!

              33 min
            • Augmenting reality for blind people

              Today we meet with Camilla Longden (@camillalongden). Camilla is a research software engineer at Microsoft. I met Camilla at an RSE workshop in London early 2020, where she presented her work in AI and machine learning. Camilla’s ambition is to create tools that improve and enhance our lives. Judging by the exciting work she does at project Tokyo she has a good chance of achieving her goal. The aim of the project is to help visually impaired people, particularly children and young adults, using augmented reality. As part of our discussion we touch on the important subject of ethics in AI/ML. As Camilla says, it “starts at the team level”.

              27 min
            • We've been around a while!

              How long have Research Software Engineering groups been around? How do you

              organically grow a group at your institution? This week we talk with Charles
              Ferenbaugh, a computational scientist at Los Alamos National Lab. Charles
              has rich experience from industry to national labs, and offers some
              interesting insights on the matter. Oh, and we also talk about his favorite ice
              cream too. We hope you enjoy the conversation!

              22 min

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