Our Team

Aron Ahmadia works at the intersection of applied mathematics, software engineering, and application domains as diverse as adaptive optics, semiconductor lithography, and ice-sheet modeling. His focus is in the collaborative development of robust, reproducible, and scalable software tools for computational science.

Joshua Ainsley is a Postdoctoral Scholar at Tufts University, where he applies bioinformatic and machine learning approaches to neuroscience research aimed at better understanding learning and memory. As someone who had to slowly gain programming skills to understand the large biological data sets generated by his research, he is excited to make the process a bit easier for others.

Carlos Anderson is a Ph.D. candidate in Evolutionary Biology at Michigan State University, where he is studying the genetic mechanisms of speciation using artificial life. He obtained his B.S. in Computer Science and M.S. in Biology at the University of Central Florida.

Jorge Aranda obtained his Ph.D. in Computer Science at the University of Toronto. He is now a postdoctoral researcher at the University of Victoria, where he studies coordination and communication in software teams.

Dhavide Aruliah is an associate professor at the University of Ontario Institute of Technology in Oshawa, Ontario. His research interests are in scientific computing, specifically in computational inverse problems, numerical linear algebra, and the numerical solution of PDEs.

Camille Avestruz is a PhD candidate and National Science Graduate Research Fellow in the Physics Department at Yale University. She uses numerical simulations to study clusters of galaxies; in particular, she is interested in how active black holes affect galaxy cluster evolution. Camille is also active in a number of outreach activities and is committed to promoting diversity in STEM fields.

Diego Barneche is a macroecologist who is passionate about global patterns of diversity, macroevolution, and statistical and mathematical modelling. He loves learning and improving his programming skills for science.

Nichole Bennett is a Ph.D. candidate in Ecology, Evolution, and Behavior at The University of Texas at Austin, where she is studying climate change impacts by investigating local adaptation and thermal biology in a butterfly-plant system. During fall semesters, she organizes a weekly informal Introduction to Biological Statistics Course. She also hosts a weekly science radio show They Blinded Me With Science on 91.7FM KVRX Austin and coordinates Science Under the Stars, a free, outdoor lecture series that helps graduate students communicate their research to the public.

John Blischak is a graduate student at the University of Chicago. His research focuses on the transcriptional response of human macrophages to infection by Mycobacterium tuberculosis. He greatly benefited from attending a Software Carpentry boot camp and enjoys passing along these useful skills to other scientists.

Azalee Bostroem is a Senior Research and Instrument Analyst at the Space Telescope Science Institute. She is primarily responsible for organizing the development of the calibration pipelines of the two spectrographs on the Hubble Space Telescope (the Cosmic Origins Spectrograph and Space Telescope Imaging Spectrograph). She also collaborates on a project using the Space Telescope Imaging Spectrograph to derive the properties of massive stars.

Erik Bray is a software engineer in the science software branch at Space Telescope Science Institute, where he works primarily on supporting Hubble and JWST science software. His software experience ranges from web development to kernel hacking, and in his "free" time he's working on an MS in Applied Physics.

Amy Brown handles communication and scheduling for Software Carpentry. In her other life, she's a freelance editor and self-publishing consultant, raises two girls, and sings as often as possible.

C. Titus Brown is an assistant professor at Michigan State University in the CSE and Microbiology departments, where he works on data-driven biology

Jennifer Bryan is an Associate Professor in the Statistics Department and the Michael Smith Laboratories at the University of British Columbia in Vancouver. She's a biostatistician specialized in genomics and takes a special interest and delight in data analysis and statistical computing.

Abigail Cabunoc is a software developer at the Ontario Institute for Cancer Research. She is currently the technical lead on the WormBase website where she uses the web to help the scientific research community. She believes in open source and open science.

After 13 years of slogging in the software industry trenches, Rosangela Canino-Koning returned to university to pursue a PhD in Computer Science and Evolutionary Biology at Michigan State University. In her copious spare time, she reads, hikes, travels, and hacks on open source software.

Chris Cannam is a software developer with the Sound Software project at Queen Mary, University of London. He has had extensive experience as a commercial software developer and on numerous open source applications, particularly in the music and audio fields.

Shreyas Cholia works on science gateway, web and grid technologies for the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, where he works to make high-performance scientific computing more transparent and accessible. He went to Rice University where he studied Computer Science and Cognitive Sciences.

Adina Chuang Howe received her PhD in Environmental Engineering. She is currently a postdoctoral research scientist at Michigan State University, where she uses skills learned from Software Carpentry to study microbial communities in the environment.

Neil Chue Hong is Director of the Software Sustainability Institute, and is based at the University of Edinburgh. His research interests are in community engagement and development, software sustainability, and the integration and analysis of data.

Stefano Cozzini is half split between CNR/IOM, where he coordinates all the center's HPC activities, and its small start-up company, where he tries to promote HPC to a wider audience. He enjoy teaching IT and HPC all around the world.

Karen Cranston is the Training Coordinator and Informatics Project Manager at the National Evolutionary Synthesis Center (NESCent). She is an evolutionary biologist interested in phylogenetic methods, phyloinformatics and an evangelist for data sharing and data interoperability in biology. Karen is the lead PI of Open Tree of Life, an NSF-funded project to synthesize published evolutionary trees.

Steve Crouch is a software architect at the Software Sustainability Institute, and is based at the University of Southampton. He assists researchers and their communities by consulting on software that is integral to their research.

Emily Davenport s a graduate student in the Department of Human Genetics at the University of Chicago. Her research interests took her from a purely wet-lab biology background to dry-lab, computational territory while studying the human microbiome and genomics.

Matt Davis is a software engineer at DataPad where he works on all levels of the application stack. In his previous jobs he worked at the Space Telescope Science Institute and NASA Goddard. Matt likes to write open source Python and help bring programming to everyone who needs it.

Neal Davis is the Training Coordinator for Computational Science and Engineering at the University of Illinois at Urbana-Champaign, where he conducts training across a range of traditional engineering software programs and packages. His professional interests include engineering pedagogy, the foundations of computing, and the history of science.

Ross Dickson has a Ph.D. in computational chemistry, and has been back and forth between academia and the software development industry a few times over the years. Now he helps profs, post-docs, and students in Atlantic Canada solve research problems involving high-performance computers.

Jonah Duckles is a data scientist with the University of Oklahoma's IT informatics group, specializing in geospatial analysis, ecological forecasting and data management. He holds a BS in Physics and an MS in Forestry and Natural Resources, both from Purdue.

Jonathan Dursi is an astrophysicist with twenty years' experience in computational science. He has taught courses in computing from the desktop to supercomputers in Canada, the US, and South Africa. In 2000, as part of the US DoE ASC Flash team, he won a Gordon Bell Award, one of supercomputing's highest accolades.

Justin Ely is a Research and Instrument Analyst at the Space Telescope Science Institute where he supports the science operations of the Hubble Space Telescope. Primarily, he uses Python to monitor and improve the performance of the two on-board spectrographs, the Cosmic Origins Spectrograph and the Space Telescope Imaging Spectrograph.

Richard Enbody is an Assistant Professor at Michigan State University. He earned his Ph.D. in Computer Science at the University of Minnesota in 1987 and his B.A. in Mathematics at Carleton College in 1976. His primary research interest is in computer security. Together with Bill Punch he wrote The Practice of Computing Using Python with editions in Python 2 and Python 3 and a translation in Chinese.

Daniel Falster is a post-doc at Macquarie University in Sydney, Australia. He uses a combination of math, computer models, and large data sets to test fundamental ideas about the processes shaping terrestrial vegetation and plant diversity. He is passionate about science, open data, reproducible research, and teaching biologists to code.

Luis Figueira is a software developer with significant experience working in research environments. He graduated as an electrotechnical engineer, specialising in speech processing. For the past 3 years he's been working in the SoundSoftware project, based in the Centre for Digital Music, Queen Mary University of London, helping researchers from the audio and music fields to build more robust and reusable research software.

Julián García is a computational scientist with interested in social and biological systems. He works as a postdoctoral fellow at the Max Planck Institute for Evolutionary Biology, where he uses computers to understand the evolution of social behavior. Before moving to Germany he lived in Colombia and the Netherlands.

Molly Gibson is a Ph.D. candidate in Computational & Systems Biology at Washington University in Saint Louis. Her research focuses on the ecological resistance and resiliency of microbial community structures and functions to perturbation by antibiotic treatment.

Ivan Gonzalez is a condensed matter physicist living in Boston. After learning a lot from the Software Carpentry on-line lessons, he now enjoys teaching others.

Julia Gustavsen is a PhD student at the University of British Columbia in Biological Oceanography. Her thesis work focuses on the changes that take place in marine viral communities over time and space. She received her BA and BSc from the University of New Brunswick.

Richard "Tommy" Guy is a PhD student in Computer Science at the University of Toronto. While at Wake Forest University, he helped create Verbal Victor, an app to help children with communication difficulties.

Steven Haddock is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at U.C. Santa Cruz, studying bioluminescence and biodiversity of marine zooplankton. He co-authored Practical Computing for Biologists with Casey Dunn.

Mike Hansen is a PhD student in Computer Science and Cognitive Science at Indiana University. His research interests include quantifying the complexity of software using cognitive models of programmers. He has designed and developed software professionally for almost ten years, and enjoys teaching others the skill and art of programming.

Ted Hart is a post-doc at the University of British Columbia where he studies the evolution of sociality in spiders using individual based models and evolutionary algorithms. He received his PhD from the University of Vermont and is a member of the rOpenSci development group.

Josh Herr is a post-doctoral researcher at Michigan State University in the Department of Microbiology & Molecular Genetics. He holds a B.S. in Biochemistry, M.S. in Plant Biology, and a Ph.D. in Integrative Biology. His research interests introduced him to phylogenetics at the command line and he has transitioned from the lab bench (almost entirely) to the computational analysis of microbial genomes and metagenomes. Josh blogs about his research interests at Cyme & Cystidium and is an editor at the bioinformatics help forum Biostar.

Konrad Hinsen is a theoretical physicist by training who currently works on protein structure and dynamics and scientific computing at the Centre de Biophysique Moléculaire in Orléans (France) and at the Synchrotron Soleil in Saint Aubin (France). He is also a department editor for Computing in Science and Engineering.

Chris Holdgraf studies cognitive and computational neuroscience at UC Berkeley. He is interested in linking higher-level theories of the mind with information processing in the brain, currently exploring how we make sense of noisy or incomplete auditory information. He also writes for and co-manages The Berkeley Science Review and co-organizes Beyond Academia.

Katy Huff is a postdoctoral scholar in nuclear engineering at the University of California – Berkeley. She received her Ph.D. from the University of Wisconsin – Madison, where she helped found The Hacker Within.

Damien Irving is a PhD candidate in Meteorology at the University of Melbourne, where his research focuses on the climate of the high southern latitudes. He also works part time with the Information Technology Services (Research) department at the University, assisting geoscience researchers with their computing. In his spare time, Damien blogs about research best practice in the weather/climate sciences.

Paul Ivanov is a graduate student in the Vision Science program at UC Berkeley. His interests include eye tracking, GPGPU programming, and natural image statistics.

Mike Jackson has a background in human-computer interaction and is a software architect at the Edinburgh Parallel Computing Centre. He is also a consultant with the Software Sustainability Institute.

Jessica Kerr has channeled an undergraduate physics degree into a programming career. She loves computer science, especially when it intersects with math and complexity theory. Her goals include acquiring new tastes, sharing enthusiasm, and keeping two crazy-happy children alive.

W. Trevor King is a freelance software developer who moonlights as an evangelist for open source software in general, and Git and Python in particular.

Justin Kitzes is a postdoc in the Energy and Resources Group at the University of California, Berkeley. His research centers on the intersection of quantitative ecology and conservation biology, with a focus on developing general methods to predict spatial patterns of biodiversity in human-altered landscapes.

Steven Koenig is studying the production of microbial exopolysaccharides using renewable resources at Technische Universität München, Straubing Center of Science, Chair of Chemistry of Biogenic Resources as a Ph.D. candidate.

Bernhard Konrad is a PhD student in Mathematical Biology at the University of British Columbia. He studies early within-host events after HIV exposure and how treatment or a vaccine could prevent infection. He received his Masters at the Karlsruhe Institute of Technology in Germany, where he focused on functional analysis.

Karin Lagesen has a PhD in bioinformatics and has since focused on the processing of high throughput sequencing data in various forms. With a background in both computational science and molecular biology, she has taught programming and computational analysis to both master and PhD students and believes that this should be an integral part of any biologist's toolbox.

Ian Langmore is a mathematician/engineer working as a data scientist in New York City. He currently works at Johnson Research Labs and teaches an Applied Data Science class in the Department of Statistics at Columbia University.

Chris Lasher works at the interfaces of molecular biology, computer science, and software development. In 2007, he lead a weekly Software Carpentry boot camp at Virginia Tech for postdocs and graduate students. To this day, Chris continues to improve his good programming habits and extol the virtues of Python, his most beloved programming language.

Doug Latornell is a professional engineer with post-graduate degrees in experimental and computational fluid mechanics and modeling and control of robotic manipulators. He works for Nordion in Vancouver, where he helps produce medical isotopes by proton irradiation from cyclotrons. Side projects include work on a coupled biology and physics model of deep estuaries that, through the winter months, calculates a daily prediction of the date of the first spring phytoplankton bloom in the Strait of Georgia.

Over the last 10 years, Luke Lee has written software for everything from Python desktop and web applications to embedded C drivers for solid state disks. He currently writes scientific Python applications for Blueback Reservoir in Houston, Texas, and is an active member of the Houston Django and Python user groups.

Yuxi Luo is a graduate student at LanZhou University. He loves data science, especially applying knowledge to solve problems in diverse areas. He believes that he can learn more when teaching others.

Cam Macdonell is a faculty instructor at in the Department of Computer Science Grant MacEwan University in Edmonton, Alberta. His teaching and research relate to operating systems, software engineering, cloud computing and virtualization.

Stephen McGough is the Research Manager for the Digital Institute at Newcastle University. His research interests lie in the areas of high performance and high throughput computing along with their implications for green computing.

Jessica McKellar is a kernel engineer living in Cambridge, MA. She is a Python Software Foundation board member and an organizer for the largest Python user group in the world. With that group she runs the Boston Python Workshops for women and their friends—an introductory programming pipeline that has brought hundreds of women into the local Python community and is being replicated in cities across the US.

Emily Jane McTavish is a PhD student at the University of Texas studying the complex evolutionary history of Texas Longhorn cattle using genomic data. In May 2013 she is starting a postdoc at University of Kansas developing tools for updating and revising the tree of life, as part of the Open Tree project.

Ian M. Mitchell is an associate professor in the Department of Computer Science at the University of British Columbia. His research interests include scientific computing, cyber-physical systems, formal verification, and reproducible research.

Jason Montojo received his Master's degree in Computer Science from the University of Toronto in 2009. He currently works for the GeneMANIA team.

Ben Morris is a Ph.D. student in the Department of Biology at the University of North Carolina. His research uses large datasets and ecoinformatics to answer questions about patterns in species distribution and community assembly. He also develops open source software to make ecology and biodiversity data more accessible.

Lex Nederbragt is a self-taught bioinformatician working with high-throughput DNA sequencing data at Oslo University, Norway. His speciality is the assembly of genomes from short pieces of sequence information.

Randy Olson is a Computer Science graduate research assistant at Michigan State University in Dr. Chris Adami's lab specializing in artificial intelligence, artificial life, and evolutionary computation. He runs a research blog where he writes about scientific computing, data visualization, evolution, and AI. Randy is an ardent advocate of open science and regularly travels the U.S. to teach researchers scientific computing skills at Software Carpentry workshops.

Aleksandra Pawlik works for the Software Sustainability Institute at the University of Manchester and is responsible for supporting scientific software communities development. She's also finishing her PhD about documentation in scientific software.

Jason Pell is a Ph.D. student in Computer Science and Quantitative Biology at Michigan State University who is primarily interested in tackling large next-generation DNA sequencing datasets. He holds a B.A. in Computer Science from Grand Valley State University.

Fernando Perez is a research scientist at the Helen Wills Neuroscience Institute at U.C. Berkeley. His work involves the development and implementation of new algorithms and tools for neuroimaging, with a special interest in functional MRI. He is also actively involved with the development of new tools for high-level scientific computing, mostly using the Python language.

Giacomo Peru is a project officer at the Software Sustainability Institute. He helps with administration and coordination of bootcamps in the UK. His background is in Classics (Università di Sassari) and in European Studies (Rome).

Marian Petre is a Professor of Computing at the Open University. She holds a Royal Society/Wolfson Research Merit Award in recognition of her research on expertise in software design. With degrees in both Psycholinguistics and Computer Science, Marian's research spans empirical studies of software development, representation and visualisation for software design, psychology of programming, human-centred computing, and computer science education.

Jon Pipitone completed his MSc in Computer Science at the University of Toronto in 2010. He has been active since then in a variety of scientific, environmental, and social justice causes.

Mark Plumbley is Director of the Centre for Digital Music (C4DM) at Queen Mary, University of London, and leads the SoundSoftware.ac.uk project. His work in audio signal analysis includes beat tracking, music transcription, source separation and object coding, using techniques such as neural networks, independent component analysis, sparse representations and Bayesian modeling.

Karthik Ram is a quantitative ecologist at UC Berkeley broadly interested in the structure and dynamics of food webs in terrestrial systems. He blogs at Inundata, and is also the co-founder of rOpenSci, a project which aims to foster reproducible research and data reuse through open source software tools.

Ariel Rokem is a post-doctoral researcher at the Stanford Psychology Department. His research focuses on the functional neuroanatomy of the human visual system. Since his time as a PhD student at UC Berkeley, he has been involved in developing open source software for neuroimaging.

Jory Schossau is a Ph.D. student at Michigan State University studying evolution through simulation, complexity measurement, and game theory. He is also involved in various outreach and education projects from educational game design to classroom teaching.

Anthony Scopatz has a PhD in Mechanical and Nuclear Engineering from the University of Texas at Austin, and is now a post-doc in the Astrophysics Department's FLASH Center at the University of Chicago.

Michael Selik is a data scientist at Infochimps. Over his career, he has worked for major enterprises and venture-backed startups delivering sophisticated analysis and technology project management services from hyperlocal demographics inference to market share forecasting. He received a MS Economics, a BS Computer Science, and a BS International Affairs from the Georgia Institute of Technology.

Jeff Shelton is a PhD candidate in Mechanical Engineering at Purdue University, studying the control aspects of human motion. Following more than two decades in industry, he is interested in aligning educational methods with the evolving societal roles performed by engineers.

Raniere Silva is a undergraduate of applied mathmatics of University of Campinas working with linear programming. His focus is in free/open software for the collaborative development of robust, reproducible, and scalable software tools for computational science and open science/access.

Rachel Slaybaugh is an Assistant Professor of Nuclear Engineering at the University of California Berkeley where she develops radiation transport methods for application to reactors, shielding, and nuclear security applications. Rachel writes in C++, Python, and Fortran, and has research experience with massively parallel code systems.

Joshua Ryan Smith specializes in electronic devices based on wide-bandgap semiconductor materials and in the past has done work in surface science and nanofabrication. Joshua is a native of North Carolina and received his Ph.D. in physics from North Carolina State University; he learned Python programming in graduate school and has an interest in understanding the design of experiments in terms of the practices of software development.

Sarah Supp received her Ph.D. student in Ecology from Utah State University. Her research interests lie in combining field studies, macroecological analyses and ecoinformatics to understand the dynamics that drive change at the community and ecosystem level.

Tracy Teal is a bioinformatics specialist at Michigan State University, having completed an NSF Postdoctoral Fellowship in Biological Informatics. She has developed open-source tools for metagenomics analysis and, as a member of the Great Lakes Bioenergy Research Center, studied the effects of land use change on microbial communities and greenhouse gas flux.

Ramnath Vaidyanathan is an Assistant Professor of Operations Management at McGill University. He holds a PhD in Operations Management from the Wharton School, and has worked at McKinsey and Company. He is addicted to R and has developed two R packages, Slidify and rCharts, both aimed at simplifying the creation and sharing of interactive web-based content with R.

After working as a Python software engineer, Nelle Varoquaux returned to university in 2011 to pursue an applied mathematics degree, specializing in machine learning. She is now using her skills to solve biological problems, such as reconstructing the 3D architecture of the genome.

Bogdan Vera is a PhD student in the Centre for Digital Music, at Queen Mary University of London, and previously studied at the University of York and Bournemouth University. His research is about distributed music technologies that can enable musicians to more effectively perform and compose music over great distances using the internet.

Alex Viana is a Research and Instrument Analyst at the Space Telescope Science Institute where he supports the operations of the Hubble Space Telescope. Primarily working in Python and SQL he has contributed to a wide range of scientific and educational projects at STScI.

Jens von der Linden is a PhD student in plasma physics at the University of Washington. He is designing and building an experiment to simulate astrophysical jets in the lab. His focus is the interaction between twisted magnetic fields and twisted flows in the jets and their stabilizing effects. He uses Python for data analysis, and has also worked on plasma fluid simulations in Fortran and Python.

Ben Waugh writes and maintains software, teaches programming and a bit of physics, manages computer systems and drinks lots of coffee in the Department of Physics and Astronomy at University College London, mostly in the High-Energy Physics Group.

Ethan White is an Associate Professor in the Department of Biology and the Ecology Center at Utah State University. He is a recipient of the prestigious National Science Foundation CAREER "Young Investigators" Award. He is a proponent of open and reproducible science and serves on the editorial boards of both PLOS ONE and PeerJ.

Lynne Williams works at the Rotman-Baycrest Research Institute, where she studies the cognitive neuroscience of language development over the lifespan and develops statistical techniques to analyze large multivariate data sets. Her most recent work is concerned with pattern classifiers in brain imaging and age-associated patterns of variability in brain activation.

Greg Wilson started the Software Carpentry project in 1998. He has been a professional software developer, an author, and a university professor. Greg received his PhD in Computer Science from the University of Edinburgh in 1993.

Paul Wilson is an Associate Professor at the U. Wisconsin-Madison where he teaches nuclear engineering. His research group, CNERG, delivers new capability for the simulation of nuclear systems. The Hacker Within was born from his research group as he tried to impart Software Carpentry skills upon his graduate students.

Christopher Woods is a researcher at the University of Bristol, where he develops software for modelling medicinal drugs and proteins. He obtained his PhD in physical chemistry at the University of Southampton, where four years hacking through established academic codes gave him a keen appreciation of the importance of clean design, good documentation, testing and version control.