Programming Fundamentals and Bioinformatics in R


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Experimental CPSC 499 course for second half of fall semester 2017

This course is aimed at graduate students who have been briefly introduced to R in their coursework and want to understand the R programming language in more depth in order to use it in their research.  It assumes no knowledge of computer science, and will cover introductory computer science concepts and vocabulary.  Students will learn to create their own R functions, and will create small R packages as a final project.  The course will also introduce analysis of DNA, RNA, and protein sequence data using BioConductor.

Lecture 9:30-10:50am Tuesday/Thursday. Lab/Discussion 11:00- 12:20pm Tuesday

2 Credit Hours; CRN 69380

Instructor: Lindsay Clark


Illinois faculty and staff can request time on Blue Waters supercomputer

Blue Waters is one of the world’s most powerful computing systems and is located at Illinois. Each year more than 3 million node-hours are allocated to projects from our campus. Each node has many powerful cores, providing University faculty and staff significant computing power. Proposals are accepted twice per year, the next deadline is September 15, 2017. More information can be found at

NCSA processes big data with breakthrough results for Dark Energy Survey

New measurements from data processed by the Dark Energy Survey Data Management (DESDM) project at the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign verify the theory that 26 percent of the Universe is in the form of mysterious dark matter and that space is filled with an also-unseen dark energy, which is causing the accelerating expansion of the universe and makes up 70 percent of the Universe’s contents.

To read the full story, visit

rOpenSci Fellowships Available

rOpenSci has three Fellowships available. Deadline to apply Sept 1, 2017.

rOpenSci promotes a culture of open, transparent, and reproducible research across various research domains. Everything we do, from developing high-quality open-source software for data science and, software review, to building community through events like our community calls and annual unconference, is geared toward lowering barriers to reproducible, open science.

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Software Carpentry Workshop August 31

NCSA and CSE will host several Software Carpentry workshops in the fall term. The first is August 31. To register visit

Topics will include an introduction to Python, shell scripting (Bash), and version control with Git.  If you are planning workshops which rely on any of these topics, this is a good chance to make sure prospective students are prepared.

For questions email

LabVIEW CLAD Certification Training Available

LabVIEW CLAD Certification Training is available August 14-18. This training, which typically costs $8,000 is being offered to Illinois faculty, staff and students for only $30. LabVIEW is a “systems engineering software for applications that require test, measurement, and control with rapid access to hardware and data insights.”

Registration is required by August 1, 2017. For more information and to register visit the Illinois WebStore.

Presentation: Research Data Services at Cambridge

The Research Data Service is hosting a visit by Marta Teperek, the current Research Data Facility Manager at the University of Cambridge, from July 13-14. She’ll be presenting on their data services program on Friday, July 14, and all are welcome to attend.


2:00 PM Friday, July 14th

Commons at Grainger Library (Second Floor)


How to make research data services work? How to create successful services which will be useful to the academic community? Marta will talk about her experience leading the development of research data services in Cambridge. She will talk about the Cambridge strategy for service development and innovation, including the initial failed attempt to get the research community engaged. She will then explain specific undertaking which allowed Cambridge to become more democratic and to better engage both researchers and staff. The talk will conclude with short reflections into what worked in Cambridge, what did not go so well and what could have been done differently.


Dr Marta Teperek did a Ph.D. in molecular biology at the University of Cambridge. Having first-hand experience of problems that researchers face on a day-to-day basis, with the journals’ impact factor, and not the quality of the research process, dictating the future of their academic career, Marta decided to get professionally involved in advocating for Open Research and for better reproducibility in science. In 2015 she joined the University of Cambridge and led the creation and development of the Research Data Management Facility, supporting researchers at the University of Cambridge in good management and sharing of research data. While at Cambridge, Marta initiated and overseen the Data Champions programme and the Open Research Pilot. In August 2017 Marta will move to TU Delft in Netherlands, where she will lead the Research Data Stewardship project.