Genomics & Bioinformatics Core Facility

REACT Program

UPDATE 4/18/18: All REACT funds for the 2017-18 academic year have been awarded. Thanks to all our sponsors and REACT fellows for making this program a great success. Please check back for future funding opportunities.

 

We’re happy to announce a new program, REACT (Rapid Exposure to Advanced Computational Training), to support PhD students hoping to gain external training in computational tools and techniques.

REACT is a joint effort of the Environmental Change Initiative (ECI), The Eck Institute for Global Health (EIGH), and the Genomics and Bioinformatics Core Facility (GBCF). REACT will provide up to $1,500 to cover student tuition, registration, room and  board to attend nationally-recognized workshops that provide the training in the latest computational approaches. REACT is a short-term program; applications are considered on a rolling basis starting today January 4th, 2017, and funds will be dispersed until they run out.

REACT is indented to help you learn to generate, manipulate, and analyze data directly related to your PhD thesis. We hope that participation in these workshops will help you build networks with experts in the field and fellow peer investigators. Expertise in computational skills is in high demand on the job market, and participation in these workshops may help you compete for top jobs in academic, agency and industrial settings. 

Information on student eligibility and application instructions are listed below.

Any questions can be directed towards

Elizabeth Archie (website)
Associate Professor Department of Biological Sciences
Behavioral Ecology and Disease Ecology
Michael E. Pfrender
Director Genomics Core Facility
Associate Professor Department of Biological Sciences
Evolutionary and Ecological Genomics

pfrender.1@nd.edu

Dr. Katherine Taylor (website)
Associate Director and Director of Global Health Training, EIGH
Master of Science in Global Health
Ktaylo12@nd.edu

 

PROGRAM ANNOUNCEMENT

REACT: Rapid Exposure to Advanced Computational Training

Across the sciences, the skills required to analyze large data sets, build statistical models, and simulate complex processes are becoming increasingly critical. For example, genomic data sets may consist of millions of sequencing reads from hundreds or thousands of samples. In ecology and earth sciences, researchers are applying new methods for modeling ecological data and assimilating data and models to improve forecasts of ecological and environmental change. In systems biology, scientists are modeling the emergent properties of interacting genes, proteins, cells, and tissues. All of these research areas depend on computational fluency.

The REACT program (Rapid Exposure to Advanced Computational Training) is a short-term initiative to support graduate students to receive the latest training in computational tools and techniques in their field. REACT is a joint effort of the Environmental Change Initiative (ECI), The Eck Institute for Global Health (EIGH), and the Genomics and Bioinformatics Core Facility (GBCF). REACT will provide up to $1,500 to cover student tuition, registration, room and board to attend nationally- and internationally-recognized workshops that provide the training in the latest computational approaches. Such training is a top priority of many ND faculty. REACT is a temporary program, intended to quickly and efficiently train a cohort of students who will act as leaders in computational approaches and serve as a support network for each other and their labs. Applications are considered on a rolling basis, and funds will be dispersed until they run out.

Eligibility

  • The applicant must be a PhD student enrolled at Notre Dame.
  • The student's advisor/PI must be a member in good standing with either the Environmental Change Initiative, the Eck Institute for Global Health, or Notre Dame’s Genomics and Bioinformatics Core Facility. Students should check with their advisors if they are unsure.
  • Students attending workshops may be asked to share the knowledge they gain with local working groups, journal clubs, or classes.
  • REACT only covers costs for registration, tuition, room and board, up to $1,500. REACT does not cover research expenses or travel costs. Travel costs are expected to be covered by the student’s advisor/PI.

Application instructions

  1. Applications are considered on a rolling basis.
  2. Applications and inquiries should be submitted to Beth Archie (earchie@nd.edu), Mike Pfrender (pfrender.1@nd.edu), or Kathy Taylor (ktaylo12@nd.edu).
  3. Applications should consist of 2 parts:
  1. A one-page application that explains:
    1. What workshop the student plans to attend
    2. Whether you have already been admitted to the workshop (e.g. the student has not yet applied, the student has applied and the application is pending, or the student has applied and has been admitted to the workshop)What computational skill(s) they will learn at the workshop
    3. How those skills will help their research
    4. A short budget that states the cost for workshop registration, tuition, and room and board. REACT provides up to $1,500 to cover these costs and these costs only.
  2. A short letter from the student’s sponsoring advisor/PI that states:
    1. That the PI supports the student’s attendance at the workshop
    2. That the PI will pay for the student's travel costs
    3. Which of the following ND Centers, Initiatives, and Institutes the PI regularly affiliates with: ECI, EIGH, or GBCF.
    4.  
To date we have supported training for seven students to attend six different courses in four different countries! Read below to see what courses they attended and what they thought of the experience.
 
Mauna Dasari - Strategies and Techniques for analyzing Microbial Population Structures (STAMPS) Workshop. Mauna Says, "STAMPS provides a great platform for networking and collaboration. As a graduate student with a solid theoretical basis in microbial ecology, this course was... a useful way to learn about the variety of software available...Thanks to this method of instruction and the large amount of lab/tutorial time provided, I learned about the intent, mathematical basis, and potential limitations of each piece of software and how it could potentially be applied to my data."

Brandon Gerig - Stable isotope mixing model training workshop being offered by PR Statistics in Scotland. Brandon says, "The REACT fellowship provided me with integral support to pursue a workshop focused on understanding and implementing Bayesian Stable Isotope Mixing Models. The funding facilitated a very targeted, specialized training that was directly related to my research focused on understanding food web dynamics and contaminant accumulation in freshwater food webs. The benefit of REACT in my opinion is that it allows for the student to rapidly develop a specialized quantitative skill set without having to take a traditional semester long course which may or may not directly relate to the students research. On a side note, having the workshop hosted in Europe also provided me with opportunities to network with other researchers using isotope approaches from the EU, South America, and Africa thus expanding my horizons to consider international research in the future."

Kyle Dubiak & Elizabeth Peuchen - 2017 Xenopus Bioinformatics Workshop in Orsay, France. Elizabeth says, "After this course, I am able to code at a basic level using AWK, Unix, and Matlab (had previous experience with Matlab). Another very valuable tool I was able to learn at the course was how to process RNA data from the raw fastq file to eventually generating expression level values of the sample". Kyle says, "Before coming to this workshop, I had little to no experience in computational data analysis, with only about two months of experience in using Matlab for coursework here at Notre Dame. But by the end of the course, I had learned a tremendous amount."

Rachel Oidtman - attended Meaningful Modeling of Epidemiological Data at the African Institute of Mathematical Sciences in South Africa. Rachel says, "I learned important statistical and epidemiological skills that are necessary for my studies of disease modeling and disease ecology... Besides the skills that I learned, I had the opportunity to work on a collaborative project with students from both African and American institutions, which resulted in a report that could eventually lead to a publication. Lastly, the best takeaway from this clinic were the relationships I formed and potential collaborators I met. I can see myself collaborating in the future with several of the other attendees and also the professors and post docs that were in attendance."

Chissa Rivaldi - Environmental Genomics Workshop at MDI Biological Lab in Bar Harbor, ME. Chissa says, "This workshop was very beneficial to my development as a scientist – the subject matter is not particularly well suited for a long-semester class, but even if it was, I think it’s specialized enough that I wouldn’t expect to see a similar course offered in my department."

Sage Davis - The Summer Institute for Statistical Genetics (SISG) at the University of Washington, School of Public Health. Sage was able to take four modules, including Advanced Population Genetics, Association Mapping Case Study, Integrative Genomics, and Pathway and Network Analysis for Omics Data. Sage says, "The Summer Institute for Statistical Genetics (SISG) at the University of Washington provided a wonderful opportunity to not only learn new computational methods unavailable at the University of Notre Dame, but also to interact with students, postdocs, techs, and PIs who are also in the forefront of computational genetic research".

AVAILABLE WORKSHOPS

Please see the list of available workshops: 2017 Analysis Workshops

Don't see a program you are interested in? Let us know