ºìÌÒÊÓƵ

The CompBio Lab

People

Anna Ritz (PI)
I joined the ºìÌÒÊÓƵ Biology Department in the Fall of 2015. For more information, see the home page, my CV, or the links on the right-side banner.
Current Members
Pramesh Singh, postdoctoral researcher
Alumni
Nick Franzese, post-bac researcher
Alexander King, post-bac researcher
Amy Rose Lazarte, post-bac researcher
Darsh Mandera, high schooler
Ramin Neshati, visiting scholar
Gabe Preising, post-bac researcher
Alex Richter, post-bac researcher
Tobias Rubel, post-bac researcher
Ibrahim Youssef, postdoctoral researcher
Summer 2022: Hannah Kuder (Math/Physics), Henry Jacques (Biochemistry), Li Yi (Math/CS), Nina Young (CS/Art), Larry Zeng (Math/CS)
Summer 2020: Jiarong Li (Math/CS). Alex Richter (Math/CS), Aryeh Stahl (Math/CS), Larry Zeng (Math/CS), Frank Zhang (Biology)
Summer 2019: Tayla Isensee (Biology), Tunc Kose (Math/CS), Jiarong Li (Math/CS), Karl Young (Biology)
Summer 2018: Miriam Bern (Biology), Alexander King (Neuroscience), Sol Taylor Brill (Biology), Kathy Thompson (CS), Usman Hafeez (Math)
Summer 2017: Nick Egan (Sociology), Giorlando Ramirez (Economics), Yurel Watson (CS)
Summer 2016: Karl Menzel (Biology)

Group Photos

2022 ice cream

2022 group taking advantage of hot weather + ice cream. From left to right: Li Yi, Henry Jacques, Larry Zeng, Anna, Max Bennett, Nina Young, Alex Richter.

2022 poster 1 2022 poster 2

2022 group members presenting at the ºìÌÒÊÓƵ Fall Poster Session. Left: Li Yi and Hannah Kuder; Right: Henry Jacques and Max Bennett.

2022 dinner

2022 Group Dinner! From left to right: Nina Young, Alex Richter, Pramesh Singh, Larry Zeng, Anna, Li Yi, Henry Jacques, Max Bennett, Hannah Kuder.

2020 croquet

2020 was mostly a mostly remote summer, except for an excellent croquet match. From left to right: Anna, Larry Zeng, Jiarong Li, Frank Zhuang, Alex Richter, Gabe Preising.

2019 ACM-BCB

Amy Rose Lazarte presents her thesis work at the 2019 ACM-BCB Conference in Niagara Falls, NY.

2019 Murdock Poster Session 2019 President's Welcome

2019 posters presented a local venues. Left: Tayla Isensee presents at the 2019 Murdock Trust Undergraduate Science conference. Right: Jiarong Li and Tunc Kose present at ºìÌÒÊÓƵ President Audrey Bilger's welcome event.

2019 OHSU Visit

2019 visit to OHSU's Knight Cancer Research Center. From left to right: Tunc Kose, Alex King, Amy Rose Lazarte, Jiarong Li, Tayla Isensee, and Karl Young.

Summer 2017 Hike

2017 Hike up Hamilton Mountain with Suzy Renn's group and other students (we're tiny!).

Spring 2016 Thesis Students

2016 Thesis student photo! From left to right: Heather Milne, Nicole Ezell, Barney Potter, and Anna Ritz.

The CompBio Lab

Located in Biology B203, the Computational Biology (CompBio) lab is a resource for Biology students working on computationally-intensive research and thesis projects.

The new B203

The lab (shown here in October 2015) now includes machines and a printer, in addition to the large display and whiteboard.

Machines

B203 houses Linux computers, including eight quad Intel Core i7-4790 processors with 16GB memory and 256GB solid state hard drives. Additionally, we have one Dual Intel Xeon E5-2680 v4 Processor (14 cores) with 128GB memory and a 512GB solid state hard drive with an extra 2TB serial-ATA hard drive for storage.

Students using the CompBio Lab will become familiar with unix-like environments and working from a terminal. Here are some places to get started.

  • ºìÌÒÊÓƵ's Computer User Services has a Unix help page with many common commands and tips.
  • This amazing walks people through tutorials, all within a web browser.
  • There are many nice command-line tools for manipulating text files.
    • grep for matching strings and patterns in text.
    • awk for rearranging columns of text.
    • sed for searching and replacing strings and patterns in text.
  • Use top to see the processes currently running on your machine.
  • To see the size of a file (or files in a directory), use ls:

    ls -lh
  • To see the size of the contents of an entire directory (e.g., mydir), use du:

    du -h --max-depth 1 mydir

Access

B203 requires key-card access. By default, all of my thesis students will get access. If you are working on a computationally-intensive project, talk to me to see if it's appropriate for CompBio Lab use.

Use your username and password to log onto the machines. Just like the computer labs in the ETC, any files saved on the local machine are erased when you log out. Use file storage systems such as AFS or Google Drive to save your work (check out Sharing at ºìÌÒÊÓƵ for a list of options. Save early, save often. Talk to me if you begin working with very large files that make this prohibitive.

You may choose to manage your projects with a versioning system such as GIT or SVN. is a popular place for hosting and managing projects (though they have a maximum upload size limit so storing data on GitHub is not ideal).

  • is a one-page quick setup tutorial.
  • The is available in other languages.
  • offers tutorials on common workflows.
  • is an interactive, example-based tutorial.
  • These and dozens of other tutorials are listed on .
Remote Access

The machines can be remotely accessed when students are off campus. Only students with swipe access can remotely log into the machines. The machines are labeled bioinf1 to bioinf8.

You must first fill out a Virtual Private Network (VPN) request form, available on the VPN Policy Page. If you want to use your personal laptop for remote access, you may need to take extra security measures in order for Information Technology to grant you access.

To log into a particular machine (e.g., bioinf5), you can ssh with

ssh username@bioinf5.reed.edu

where username is your ºìÌÒÊÓƵ login. You will be prompted for your password.

Installed Packages

To request other software, email me with the name and download page. After I check the license, I will pass it on to Computer User Services and it will be installed on the machines within a couple days. To request Python modules or R packages, simply give me the module/package name.

Software:
blasr
Long read aligner designed for data sequenced by Pacific Biosciences (PacBio).
blat
BLAST-like alignment tool.
ncbi-blast+
Suite of Basic Local Alignment Search Tools (BLAST).
synapseclient
Provides an interface to , a collaborative platform for data-intensive computational biology projects.
inkscape
Free and open-source vector graphics editor (think Adobe Illustrator without the price tag).
samtools
Utilities for the Sequence Alignment/Map (SAM) format.
Python modules:
matplotlib
A 2D plotting library.
networkx
A software package for the creation, manipulation, and study of networks.
R packages:
adgenet
Multivariate Analysis of Genetic Markers.
ape
Analyses of Phylogenetics and Evolution.
Rsamtools
Utilities for Sequence Alignment (R package).

ritz portrait

Contact

Biology Department
ºìÌÒÊÓƵ
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

Email icon aritz-at-reed-dot-edu

CV icon Curriculum Vitae [pdf]



orcid icon