The UD Bioinformatics Student Association (BiSA) hosted a Data Carpentry workshop on March 29-30. Data Carpentry is a two-day workshop on key concepts, skills, and tools for managing and working with data. They provide a variety of domain-specific curriculums including ones that focus on genomics (taught during this workshop), ecology, and geospatial data (http://www.datacarpentry.org/lessons/). There were approximately 30 attendees including graduate students and faculty from UD’s bioinformatics, biology, biochemistry, geology, animal sciences, and plant and soil sciences programs of study as well as an attendee from Delaware State University.
Instruction involved both tutorials and hands-on exercises. Topics covered included data manipulation and visualization in R, connecting to the Amazon cloud, using the UNIX command line environment, an introduction to shell scripting, and best practices in data management. The topics were taught by going through two important bioinformatics problems, sequence read quality control and variant calling, illustrating the relevance and usefulness of the covered skills.
The workshop was a success thanks to funding from the UD professors, Dr. Carl Schmidt and Dr. Cathy Wu, and the great instruction provided by the data carpentry teachers, Pariksheet Nanda and Rebecca Love. We would also like to say thank you to Erin Bernberg for giving a tour of DBI’s sequencing facilities and to Karol Miaskiewicz for giving a presentation on the computing resources provided by UD’s Center of Bioinformatics and Computational Biology (CBCB).
The BiSA administrators (President Irem Celen, Vice President Modupe Adetunji, Secretary Madolyn MacDonald, and Treasurer Mengxi Lv) organized the workshop.
Visit http://www.datacarpentry.org/ to learn more about Data Carpentry.
BiSA is hosting another ice skating event Friday 1/27 from 7-9 pm at the Fred Rust Arena. Ice skating is free with a UD ID and skate rental is $4. We hope to see you there!
We invite all BiSA members to UD's Fred Rust Ice Area for ice skating on Dec. 16th. Ice skating is from 8-10 pm and admission is free with UD student ID. Skate rentals are available for $4.
To start an iGem team at UDel, we are looking for interested students and faculty. We are hosting a presentation all about iGEM on October 25th at 4:30 PM in DBI 102. More information about the competition can be found at www.igem.org. For any questions about iGEM at UDel, please email Sam Keating at email@example.com
iGEM stands for the International Genetically Engineered Machine Competition, which aims to advance the field of synthetic biology. There are currently close to 300 universities that compete with interdisciplinary teams working inside the lab and doing computational analysis. University of Delaware does not currently have an iGEM team, but I have worked closely with an iGEM team for several years at UMBC as an undergraduate. We designed a project for heavy metal remediation using engineered E. coli and won a bronze medal. Our data went towards a mathematical model that can predict optimal enzyme concentrations to be engineered into a new cell line to give the most copper resistance.
iGEM teams have carried out a wide array of projects including aptamer discovery, CRISPR/Cas9 site optimization, 3D biofilm printers, and new transformation methods. The timeline for an iGEM team focuses on spending the most time in the lab during the summer. Registration for university teams happens around April and gene libraries are mailed out shortly after. Planning and computational predictions start when the team starts meeting early in the calendar year and continue throughout the summer leading up to the conference and competition around October.
BiSA hosted a "welcome back" picnic at Lums pond Saturday, Sept 17th at 11 am. BiSA members enjoyed kayaking on the pond as well as a provided lunch.
The following students will be the BiSA officers in 2016-2017 academic year:
President – Irem Celen
Vice President – Modupe Adentunji
Secretary – Maddy MacDonald
Treasurer – Mengxi Lv