Our next summer highlight comes from Aryeh Stahl, a rising Computer Science / Mathematics senior at Reed College. Aryeh has been working to integrate cancer data into interactomes, large graphs that describe protein-protein interactions that occur within the cell.
Read Aryeh’s post on the Reed CompBio Blog: Integrating Cancer Data into Interactomes.
Reed classes start on Monday, so stay tuned for a Summer 2020 debrief!
Our next summer highlight comes from Alex Richter, a rising Computer Science / Mathematics junior. She has been working to integrate a recently published hypergraph algorithm into a large, community driven biological network visualization tool. This has been an exciting collaboration with Dr. Guanming Wu from Medical Informatics and Clinical Epidemiology at OHSU.
Read Alex’s post on the Reed CompBio Blog: Hypergraph Algorithms.
(you can catch up with all summer research projects in my earlier Summer 2020 Research post)
In my last post I talked about the actions I plan to take to combat racism in academia and science. I have also been reading with great interest the committments from both academia and industry. Here is one example of how racism is embedded in the computing community, and how I implicitly contributed to it.
Orientation next week marks the true end of summer for Reed. For a final summer highlight, Tunç Köse shares his perspective on directed acyclic graphs (DAGs) for signaling pathway reconstructions and comparing to a shortest-paths approach. Read his post for more information: More about DAGs.
Thanks to all summer students, both returning and graduated! Here’s to a wonderful academic 2019/20 year.
Jiarong Li, a Math/CS major, is third in our series of summer research highlights. She has teamed up with Tunç Köse to design and implement an algorithm that builds increasingly larger directed acyclic graphs (DAGs) within a protein-protein interactome. We are looking to see how this algorithm reconstructs known signaling pathways. Read Jiarong’s post for more info:
Reconstructing Signaling Pathways by DAGs
(If you want to learn a bit about all projects, read my summer kickstarter post).
This fall has has been filled with meetings of all types:
Meeting 1: Pacific Northwest Quantitative Biology (PacNow QB) Meeting
Who: Organized by yours truly and Derek Applewhite.
What: Regional meeting for faculty, researchers, and students interest in quantitative, data-driven biology.
Where: Hosted at Lewis & Clark College (thanks Clarkies!).
When: September 22
Interested? The meeting has been held annually, and includes a student poster session and faculty/researcher invited talks.
Meeting 2: Computational Biology Workshop
Who: Organized by kick-ass computer scientist Layla Oesper.
What: Undergraduate workshop that brought together faculty from five liberal arts institutions to introduce computer science students to applications in biology.
Where: Hosted at Carleton College in Northfield, Minnesota (proudly known as the city of “Cows, Colleges, and Contentment”).
When: September 29-30
Interested? No immediate plans for a future workshop of this type, but all the materials are freely available online.
Meeting 3: Consortium for Computing Sciences in Colleges (CCSC-NW) Regional Meeting
Who: Organized by Kelvin Sung and others, including pretty fantastic women in CS: Tammy VanDeGrift, Haiyan Cheng, and Shereen Khoja.
What: Regional meeting for computer science educators at colleges in the Pacific Northwest, with a focus on CS education.
Where: Hosted at University of Washington, Bothell.
When: October 12-13
Interested? This was my first time and I loved meeting new colleagues. CCSC-NW is usually held in early October every year, and will be held in the Portland area next year.
And then there’s the crazy beautiful weather here in Portland – fantastic view of St. John’s Bridge in North Portland during a hike in Forest Park:
Yet another example of how sexism can creep into academia: as CMU’s business incubator became more prestigious, its female founder’s role became marginalized.
Read an interview with Dr. Blum in NEXT Pittsburgh: Lenore Blum shocked the community with her sudden resignation from CMU. Here she tells us why.
Coverage from the Pittsburgh Post-Gazette: 2 CMU computer science professors — including founder of Project Olympus incubator — resign
I will be using this in all future Computational Systems Biology courses. Thanks to Mitch Wagner at Virginia Tech for the head’s up.
A recent paper by Holman et al. in PLOS Biology presents a new look at the gender gap in publications for millions of authors from over one hundred countries in over six thousand journals. You can interact with the data through their web app.
The gender gap in science: How long until women are equally represented?
Luke Holman, Devi Stuart-Fox, Cindy E. Hauser, PLOS Biology 2018.
The authors present the current author gender ratio, its rate of change per year, and the estimate number of years until the gender ratio comes with 5% of parity. A few notes below the image…
Here are the first things I noticed:
- The estimated percent of women authors “maxes out” at 50% (there’s a Figure 2 that includes fields with a higher percentage of women).
- arXiv.org – the preprint server that began as a mathematics and physics venue – has particularly poor percent of women authors.
- First author percentages tend to be “ahead of the curve” for each discipline, while last authors lag behind the numbers for all authors. In many fields, first authors denote who did the most work, and last authors denote who funded the work. My hunch is that a higher proportion of women get papers as graduate students and postdocs, whereas fewer women make it to senior-level faculty as heads of a lab.
- On a positive note, more women are publishing in the fields than before (the rate of change is mostly positive).
The paper’s supplementary figure S3 shows data for Computer Science (from arXiv). Based on current trajectories, only two sub-categories (Information Theory and Robotics) hope to see gender parity within the next 50-100 years. We still have a long way to go.
From the blog Mike the Mad Biologist comes a summary of a NY Times article comparing the number of degrees obtained to the number of job openings for different STEM fields.
Yes, We Have A STEM Glut | Mike the Mad Biologist
The takeaway message: if you’re interested in a science field, learn some computing skills along the way.