Welcome to the Onish Summer Computing Workshop 2022!
Every summer, the Osborne-Nishimura lab does a summer workshop series, and it has grown every year! This summer we are focusing on different topics related to computer literacy and computing basics.
This year’s workshop is geared towards anyone interested in learning more about computers and computing and does not require prior computer science experience (though that never hurts). We encourgae people at all career stages (i.e. undergraduate, graduate, postdoc, PI) to attend and participate.
We will introduce computer science concepts, give you a tour of computer hardware, learn more about different programming languages, and introduce GitHub as a way to collaborate. The overall goals are that both participants and presenters learn more about computing and computers along the way, to facilitate networking and collaboration among attendess, and encourage data sharing and reproducibility.
We are very excited to host this year’s computing workshop in person! The workshop will be held on Wednesday, July 20th from 1pm to 3pm. Join us in the Molecular and Radiological Biosciences (MRB) building at CSU in room 312. There will also be a mixer afterward!
Following the workshop, we will send out a short survey to get your feedback so please keep an eye on your inbox! Also, see below under Resources for some additional training opertunities and educational resources.
Sign up form
Planning to attend? Then please complete this SIGN UP FORM to register.
Please register by July 15th if possible so that we can get an idea of attendance. If you happen to register later than that, that is also ok.
Speakers, Topics, and Schedule
Participants do not need to install or prepare anything ahead of the workshop. Bring a laptop to the workshop if you have one, but they are not required.
Naly Torres - Host
Naly will introduce the speakers and provide personality.
Jessica Hill - Intro Computing Systems and Hardware (1 - 1:30 pm)
Jessica will present an overview of computing systems, including the different types of systems, how to interact with them, and how they can be utilized for research.
Andrew Moore - Programming Languages and Their Usages (1:30 - 2 pm)
Andrew will present an overview of various types of programming languages and their usages, with an emphasis on how different languages can be applied to different research questions and problems.
David King - Installation and Package Mangement (2 - 2:30 pm)
David will present on software instillation, dealing with software dependencies during installation, and how to establish project environments with Conda.
Robert Williams - Working on GitHub (2:30 - 3 pm)
Rob will introduce GitHub as a tool and resource for researchers, how to manage data and projects on GitHub, and how to share and facilitate collaborations through GitHub. He will also discuss how GitHub can help researchers track and reproduce their data.
Mixer
Following the workshop, join us for a light mixer. Stay to meet other researchers across campus with similar interests or hangout and ask more questions.
Resources
Please check out the following resources:
A field guide to cultivating computational biology
RECOMMENDED COURSES:
- DSCI510 - Linux as a computational platform (Erin). 4 weeks in the Fall. 1 credit ##CURRENTLY FULL FOR Fall 2022; Next available Fall 2023
- DSCI511 - Python (Tai). 6 weeks in the Fall 2 credits
- DSCI512 - RNA-sequencing data analysis. 4 weeks in the fall. 1 credit
- All can be taken as a series. DSCI510 and 511 have NO pre-requisites
- The pre-req’s for DSCI512 are DSCI510 OR some background with LINUX and BASH scripting
- CM580A3 - Survey of quantitative cell and molecular biology. 1 credit. all spring semester. David King. Rotating professors. All in R
- Undergrad level courses. I also helped to put together a concentration in data science within our major. Here is the list of courses those students take. Some of the data science courses (listed in the tables at the end) may also be of interest for grads:
- https://www.bmb.colostate.edu/wp-content/uploads/sites/22/2021/09/data-science-concentration-fall-2021-fnl.pdf
- CMB also keeps a list of quantitative courses at the grad level that they recommend:
- https://cmb.colostate.edu/qcmb-curriculum/
- ERHS535 - R Programming for Research
- No prerequisites.
- Offered in the fall
- BC571 - Quantitative Biochemistry
- BC 511, may be taken concurrently.
- Offered in the spring
RECOMMENDED WORKSHOPS:
- RMACC computing conference - Boulder CO
- August 2 - 4, 2022
- https://hpcsymposium.rmacc.org/
- $30 for students; $120 everyone else
- Research Computing - UC Boulder
- https://colorado.edu/rc/userservices/training
- Throughout the year they offer several beginner-level and intermediate-level workshops (i.e., intro to HPC (High-Performance Computing) Part 1 & 2; Python for beginners part 1 & 2; Intro to Alpine (the new supercomputer at Boulder), and Intro to Jupyter 3 - from Noob to Pro)
- Morgan Library’s Cookies & Coding series (will start up in the fall):
- https://libguides.colostate.edu/coding-cookies
- Specifically for learning R
- they also have an R consultant on staff for individual needs
- Research Computing Boulder training series:
- https://www.colorado.edu/rc/events
- will start up in the fall
- in person & over zoom
- course materials from past workshops are here: https://www.colorado.edu/crdds/learning-materials
- Software Carpentry
- Data Carpentry