Karthik Ram is a research scientist at the Berkeley Institute for Data Science [1] and member of the Initiative for Global Change Biology [2] at the University of California, Berkeley. He is best known for being the co-founder of rOpenSci. [1] Ram's work focuses on global change, data science, and open research software.
Ram received his PhD in Ecology and Evolution at University of California, Davis. After his PhD, he went on to hold a post-grad position at University of California, Santa Cruz [3] before eventually moving to UC Berkeley. Currently, Karthik Ram is a research scientist at UC University of California, Berkeley for both the Berkeley Institute for Data Science and the Berkeley Initiative for Global Change Biology. His work aims to make it easier for scientists to produce reproducible research. [4]
Ram co-created rOpenSci in 2011, [3] and is currently the lead of the project. rOpenSci is non-profit with the goal of making data retrieval more accessible through open source R packages. [5] He also a member of the peer-review and editorial staff for the rOpenSci Software Review. [6] Ram is the lead principal investigator for the URSSI (US Research Software Sustainability Institute). [7] Karthik Ram has been the lead of this project since its initial grant in December, 2017. [8] Ram is a founding editor of the Journal of Open Source Software, [9] [10] and an editorial board member of ReScience C [11] and Research Ideas and Outcomes, [12] which are both academic journals focused on open research sustainability.
Among Ram's notable work are the following:
Reproducibility, also known as replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or in a statistical analysis of a data set should be achieved again with a high degree of reliability when the study is replicated. There are different kinds of replication but typically replication studies involve different researchers using the same methodology. Only after one or several such successful replications should a result be recognized as scientific knowledge.
Stanley Benjamin Prusiner is an American neurologist and biochemist. He is the director of the Institute for Neurodegenerative Diseases at University of California, San Francisco (UCSF). Prusiner discovered prions, a class of infectious self-reproducing pathogens primarily or solely composed of protein. He received the Albert Lasker Award for Basic Medical Research in 1994 and the Nobel Prize in Physiology or Medicine in 1997 for prion research developed by him and his team of experts beginning in the early 1970s.
Data sharing is the practice of making data used for scholarly research available to other investigators. Many funding agencies, institutions, and publication venues have policies regarding data sharing because transparency and openness are considered by many to be part of the scientific method.
Christopher Ray Johnson is an American computer scientist. He is a Distinguished Professor of Computer Science at the University of Utah, and founding director of the Scientific Computing and Imaging Institute (SCI). His research interests are in the areas of scientific computing and scientific visualization.
Judith P. Klinman is an American chemist, biochemist, and molecular biologist known for her work on enzyme catalysis. She became the first female professor in the physical sciences at the University of California, Berkeley in 1978, where she is now Professor of the Graduate School and Chancellor's Professor. In 2012, she was awarded the National Medal of Science by President Barack Obama. She is a member of the National Academy of Sciences, American Academy of Arts and Sciences, American Association for the Advancement of Science, and the American Philosophical Society.
The replication crisis is an ongoing methodological crisis in which it has been found that the results of many scientific studies are difficult or impossible to reproduce. Because the reproducibility of empirical results is an essential part of the scientific method, such failures undermine the credibility of theories building on them and potentially call into question substantial parts of scientific knowledge.
Srinivas Aluru is a professor in the School of Computational Science and Engineering at Georgia Institute of Technology, and co-Executive Director for the Georgia Tech Interdisciplinary Research Institute in Data Engineering and Science. His main areas of research are high performance computing, data science, bioinformatics and systems biology, combinatorial methods in scientific computing, and string algorithms. Aluru is a Fellow of the American Association for the Advancement of Science (AAAS) and the Institute for Electrical and Electronic Engineers (IEEE). He is best known for his research contributions in parallel algorithms and applications, interdisciplinary research in bioinformatics and computational biology, and particularly the intersection of these two fields.
Project Jupyter is a community run project with a goal to "develop open-source software, open-standards, and services for interactive computing across dozens of programming languages". It was spun off from IPython in 2014 by Fernando Pérez and Brian Granger. Project Jupyter's name is a reference to the three core programming languages supported by Jupyter, which are Julia, Python and R, and also a homage to Galileo's notebooks recording the discovery of the moons of Jupiter. Project Jupyter has developed and supported the interactive computing products Jupyter Notebook, JupyterHub, and JupyterLab. Jupyter is financially sponsored by NumFOCUS.
The Journal of Open Source Software is a peer-reviewed open-access scientific journal covering open-source software from any research discipline. The journal was founded in 2016 by editors Arfon Smith, Kyle Niemeyer, Dan Katz, Kevin Moerman, and Karthik Ram. The editor-in-chief is Arfon Smith, and associate editors-in-chief are Dan Katz, Kevin Moerman, Kyle Niemeyer, and Krysten Thyng. The journal is a sponsored project of NumFOCUS and an affiliate of the Open Source Initiative. The journal uses GitHub as publishing platform.
Tracy Teal is an American bioinformatician and the executive director of Data Carpentry. She is known for her work in open science and biomedical data science education.
Laura Ann Waller is a computer scientist and Ted Van Duzer Endowed Associate Professor at the University of California, Berkeley. She was awarded a Chan Zuckerberg Initiative Fellowship to develop microscopes to image deep structures within the brain in 2017 and won the 2018 SPIE Early Career Award.
Jennifer "Jenny" Bryan is a data scientist and an associate professor of statistics at the University of British Columbia where she developed the Master in Data Science Program. She is a statistician and software engineer at RStudio from Vancouver, Canada and is known for creating open source tools which connect R to Google Sheets and Google Drive.
Statcheck is an R package designed to detect statistical errors in peer-reviewed psychology articles by searching papers for statistical results, redoing the calculations described in each paper, and comparing the two values to see if they match. It takes advantage of the fact that psychological research papers tend to report their results in accordance with the guidelines published by the American Psychological Association (APA). This leads to several disadvantages: it can only detect results reported completely and in exact accordance with the APA's guidelines, and it cannot detect statistics that are only included in tables in the paper. Another limitation is that Statcheck cannot deal with statistical corrections to test statistics, like Greenhouse–Geisser or Bonferroni corrections, which actually make tests more conservative. Some journals have begun piloting Statcheck as part of their peer review process. Statcheck is free software published under the GNU GPL v3.
The Berkeley Initiative for Transparency in the Social Sciences, abbreviated BITSS, is an academic initiative dedicated to advancing transparency, reproducibility, and openness in social science research. It was established in 2012 by the University of California, Berkeley's Center for Effective Global Action. It has worked with the Center for Open Science to define and promote a set of best practices for social scientists to maximize transparency in their research. BITSS has also worked to promote registered reports, supporting journals like the Journal of Development Economics in taking up the review track.
Delia J. Milliron is the T. Brockett Hudson Professor in Chemical Engineering at the University of Texas at Austin. Milliron leads a research team that focuses on developing and studying the properties of new electronic nanomaterials. Her team pursues studies on nanocrystals, nanoscale interfaces, and controlled assemblies of nanocrystals. Her team takes a systematic approach towards elucidating effects that arise at the nanoscale with a special focus on structure-property relationships.
Manuel Corpas is an Anglo-Spanish biologist and entrepreneur known primarily for his contributions to the field of Bioinformatics and Genomics. Currently Corpas is Chief Scientist of Cambridge startup Cambridge Precision Medicine, a tutor at the Institute for Continuing Education at the University of Cambridge and a lecturer at the Universidad Internacional de La Rioja. Manuel worked on the human genome from the beginning of his career, being one of the first consumers to sequence and his own genome and that of close relatives, which he published as the Corpasome. He has held positions at the Earlham Institute as Project Leader, and the Wellcome Sanger Institute, developing the DECIPHER database, a database that aids in the diagnosis of patients with rare genomic disorders.
The Carpentries is a nonprofit organization that teaches software engineering and data science skills to researchers through instructional workshops. The Carpentries is made up of three programs areas: Software Carpentry, Data Carpentry and Library Carpentry.
Katherine Snowden Pollard is the Director of the Gladstone Institute of Data Science and Biotechnology and a Professor at the University of California, San Francisco (UCSF). She is a Chan Zuckerberg Biohub Investigator. She was awarded Fellowship of the International Society for Computational Biology in 2020 and the American Institute for Medical and Biological Engineering in 2021 for outstanding contributions to computational biology and bioinformatics.
ReScience C is a journal created in 2015 by Nicolas Rougier and Konrad Hinsen with the aim of publishing researchers' attempts to replicate computations made by other authors, using independently written, free and open-source software (FOSS), with an open process of peer review. The journal states that requiring the replication software to be free and open-source ensures the reproducibility of the original research.
Shahid Naeem is an ecologist and conservation biologist and is a Lenfest Distinguished professor and chair in the Department of Ecology, Evolution, and Environmental Biology at Columbia University. Naeem is the author of Biodiversity, Ecosystem Functioning, and Human Well-Being, and has published over 100 scientific articles.
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