Repository for Coop Newsletter emails, sent quarterly to the Coop listserv. Most recent newsletters will be on top. To receive the Coop Newsletter in your inbox, please email coophelp@fredhutch.org.

Current Newsletter

October 2020 Coop News

News Items & Events

1. The Coop Team joins Scientific Computing! As of October 1, the Coop Team is now reporting to Dirk Petersen. SciComp is a part of Shared Resources, which belongs to Interdisciplinary Science Administration (ISA). We are excited to continue integrating our training and community efforts with other Shared Resources on campus.

2. Newsletter transition: Given the nature of activities in the Coop Community, we’ve moved the newsletter to a quarterly publication cycle. You can anticipate a newsletter in January, April, July, and October each year. If you have a HutchnetID, we recommend subscribing to the Shared Resources email list for updates via their monthly newsletter. See the “Stay Informed” section below for more ways to stay connected with community news! 

3. Autumn updates and other blog highlights: The Coop Blog features community announcements, technical tips about data science, and reports on scientific findings from our data-intensive research community. As a part of our transition to a quarterly reporting cycle, we share information about our quarterly goals and accomplishments (the autumn 2020 update is here). Check out our complete list of the blog archive here, including a description of core values for the Coop Community and information about our recent work with Hutch United to support Black Lives Matter.

4. Master’s-level interns in data and software engineering: Have data or software that needs work? If you’re interested in and able to hire an intern with advanced skills in informatics or software development, please contact coophelp@fredhutch.org to learn more about opportunities available through Northeastern University to hire a master’s-level intern for 4-8 months.

5. Training in computational and data methods: In recent months, we’ve focused our energy in developing fredhutch.io training materials as stand-alone, work-at-your-own-pace courses. These materials are freely available online for anyone to view, and use open-source software and data to help you get started. If your lab or research group has at least four people interested in participating in an instructor-led session, please contact coophelp@fredhutch.org to discuss scheduling options. 

6. Carpentries Instructor Training: We are pleased to announce our membership with The Carpentries will be continuing for another year! As a part of this membership, we have the opportunity to train an additional fifteen members of our community to be instructors teaching reproducible computational methods. These trainings generally take place over two whole days or four half days following the instructor training curriculum, with multiple online sessions available each month. If interested, please submit this form to indicate your interest.

Stay Informed

• Calendar of events: see upcoming events and view instructions for adding to your own calendar. 

• Online discussion forum: Check out our Slack workspace for the Coop Community to message with other researchers and staff about all things data related. Use this link to sign up, and check out this blog post for a quick-start guide to Slack.

• Fred Hutch Biomedical Data Science Wiki: Check out and contribute to sciwiki.fredhutch.org for Fred Hutch-oriented documentation and how-to’s being actively curated by Fred Hutch staff.  

• Community groups and office hours: Interested in talking with other people about code, data, and computational methods? Check out the Training, Community and Finding Help page on the Fred Hutch Data Science Wiki for more information on what groups are meeting. Office hours are generally held in Microsoft Teams in the Coop’s Office hours channel.

Archived Newsletters

June 2020 Coop News

News Items & Events

• Cascadia funding opportunity for new regional collaborations in data-intensive science. Funding is available for regional collaborations between Fred Hutch, BC Cancer, UBC and OHSU. Projects that involve data sharing across institutions, validate new computational tools or build on existing tools are encouraged. All areas of research will be equally considered. Proposals are due July 30. Please contact cascadia@fredhutch.org for more information.
  
  
• What computational training is in highest demand? In our last newsletter, we shared a survey asking for what fredhutch.io courses for computational research are most needed right now. We’ve scheduled the most-requested classes for June (see “Upcoming Trainings” below). You are welcome to continue sharing your thoughts on courses to offer and develop here. 
  
  
• We still have a few spots open for training to teach computational methods! Want to gain teaching experience and valuable professional development skills? Complete this form to apply for Instructor Training from the Carpentries. This training will take place online over two full days or four half days; a variety of possible dates between now and the end of August are available. 

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for staff who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link). 
  •  Self-led learning: Complete materials for Intro to R, Intro to Python, Intermediate Python: Programming and Intro to Git and GitHub are now publicly available online for viewing and work-at-your-own-pace learning at any time. Introductory videos for each class are in development. Outlines and materials for other classes are linked at the end of each course description. 
  •  Instructor-led sessions: Upcoming courses for the next six weeks include Intro to Git/GitHub, Intermediate Python: Programming, Data for Data Science, and Introduction to Python. Please see Hutch Learning for more information on instructor-led sessions of fredhutch.io courses, noting that online classes are separate listings from the in-person courses and include “Online” at the end of the course title. Indicate your interest in courses by using the Interest Tracking in Hutch Learning. 
  • Share your thoughts!: Have other classes you’d like to see taught? Fill out our short survey! Have other feedback? Use our comment box

Latest Coop blog posts

We blog about community announcements, technical tips about data science, and reports on scientific findings from our data-intensive research community. Highlights from the past month include:

• A discussion from Susan Glick on keeping research data secure.
• An overview of why learning to code can be beneficial to wet-bench biologists.

May 2020 Coop News

News Items & Events

• Cascadia RFA opening soon! The Cascadia Data Alliance will be opening a Request for Applications soon for collaborative projects between investigators at Cascadia-participating institutions (Hutch, BC Cancer, OHSU, UBC), collaboration is also possible under the RFA with the UW eScience Institute and Microsoft’s AI for Health data science group. Potential for funding and Microsoft Azure credits will be included. Proposals should meet two objectives: answering a scientific question and addressing a technology challenge to collaboration/data sharing. Stay tuned and contact Brenda Kostelecky (bkostele@fredhutch.org) for more details.
  
  
• Hutch Data Core strategic planning: The re-organization of the former Hutch Data Commonwealth was announced last month and the new Data Core under Shared Resources is undertaking strategic planning efforts to define scope and priorities. A Data Core Advisory Committee is being established consistent with governance for other Shared Resources. The Data Core will use the recent needs assessments and community input to inform our planning. We will keep information flowing as we progress and we welcome added input from the Hutch research community. 
  
  
• Virtual meetings for office hours and hosted groups. It turns out many folks have been using their lunch hours to take a break from their computers, so we’ve discontinued the regularly occurring lunchtime hosted community meetings (R User, Python User, and Data Visualization Groups). We still have several other regularly scheduled office hours and hosted group meetings; check our calendar and the Coop Communities Slack discussion forum for more information. As a reminder, the Coop Outlook calendar has been discontinued, so please view our instructions for adding our Google Calendar to your calendar management system.
  
  
• What computational training would you most like to see offered? This remote work time is a great opportunity for you to learn something new! Interested in learning a programming language or type of analysis? Let us know by completing this short survey. 
  
  
• Learn to teach computational methods - Want to gain teaching experience and valuable professional development skills? Complete this form to apply for Instructor Training from the Carpentries. This training will take place online over two full days or four half days; a variety of possible dates are available. 
  
  
• Early stage pilot funding from TDS-IRC. Intended for new collaborations in computationally-intensive data science, PIs are encouraged to identify a complex data problem requiring significant computational expertise and interdisciplinary collaboration.  All areas of research across Fred Hutch will be considered.  Projects must address an important scientific question and include a data analysis plan. Due May 31. Full details and application instructions.

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for staff who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link). 
  • Self-led learning: Complete materials for Intro to R and Intro to Python are now publicly available online for viewing at any time. Introductory videos for each class are in development. Outlines and materials for other classes are linked at the end of each course description. 
  • Instructor-led sessions: We have begun teaching online, real-time, instructor-led courses, with the four classes for each course taught over one or two weeks. Please see Hutch Learning for more information, noting that online classes are separate listings from the in-person courses, and include “Online” at the end of the course title. Indicate your interest in courses by using the Interest Tracking in Hutch Learning. Upcoming courses include Intro to Git/GitHub and Intermediate Python: Programming.
  • Share your thoughts!: Have other classes you’d like to see taught? Fill out our short survey! Have other feedback? Use our comment bo

Latest Coop blog posts

We blog about community announcements, technical tips about data science, and reports on scientific findings from our data-intensive research community. Highlights from the past month include:

• Updates on the Coop’s transition from the Hutch Data Commonwealth to the Interdisciplinary Science Administration.
• An overview of responsible analysis of COVID-19 data.
• Learn to host recurring meetings in MS Teams.
• Best practices for asking for coding help.
• A tale of collaboration and the struggles of data sharing detailing the work of four UW Masters in Data Science students.

April 2020 Coop News

News Items & Events

• A new home for the Coop and fredhutch.io - The decentralization of HDC has resulted in relocation of the Coop team to Shared Resources. We are grateful to three valuable team members who will no longer be working with us, and are actively evaluating our programs to determine how to adjust our activities following this loss of staffing. See this blog post for more information.

• What computational training would you most like to see offerred? This remote work time is a great opportunity for you to learn something new! Interested in learning a programming language or type of analysis? Let us know using this form. 

• Introduction to Workflow Managers & Nextflow - Starting Monday April 20th,  9:30am. A five-day training by the core Nextflow developers will be kicked off with a presentation for a general audience on workflow managers for bioinformatics and scientific computing, with a focus on Nextflow in particular. Keep an eye on the Coop calendar for details.

• TDS IRC Pilot Awards - Early stage pilot funding is available for new collaborations in computationally-intensive data science. All areas of research across Fred Hutch will be equally considered. Applications are due on 4/30/2020 at 5 pm.
  

• Learn to teach computational methods - Want to gain teaching experience and valuable professional development skills? Complete this form to apply for Instructor Training. This training will take place online over two consecutive days; a variety of possible dates are available. 

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for staff who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link). 
  • Self-led learning: Complete materials for Intro to R and Intro to Python are now publicly available online for viewing at any time. Introductory videos for each class are in development. Instructor teaching notes for other classes are linked at the end of each course description. 
  • Instructor-led sessions: We have begun teaching online, real-time, instructor-led courses, with the four classes for each course taught over one or two weeks. Please see Hutch Learning for more information, noting that online classes are separate listings from the in-person courses, and include “Online” at the end of the course title.
  • Comment box: Have other classes you’d like to see taught? Let us know!

Latest Coop blog posts

We blog about community announcements, technical tips about data science, and reports on scientific findings from our data-intensive research community. Highlights from the past month include:

• Recommendations on working from home, including tips for MS Teams and remote teamwork. 
• Report from the Python User Group: Python IDEs

March 2020 Coop News

In light of COVID-19, we are evaluating events and meetings hosted by the Coop and fredhutch.io and will send more information soon via the listserv.

News Items & Events

• CANCELED: TODAY 12-1 pm: Coop Monthly Meeting on Technical Interviews. Panelists include Joanna Muench from HutchBASE, Loren Greenen from Scientific Computing, Evan Henrich from BBE, and Abigail Gualberto from Human Resources. Thomas D1-080 (Sze). *Note this is NOT in the Coop Lab.
  
  
• CANCELED: Data Circles event on Thursday: Data Circles (formerly known as Seattle Women in Data Science) is hosting a second anniversary event on Thursday Mar 5 at Starbucks HQ from 4-6 pm. More information on the meetup page. Please RSVP on the event page or email ekadokur@starbucks.com and include your name. Organizers need to provide a list of names to the security desk.
  
  

• Accepting Applications for SciWiki Writer-Editor Program: the program engages Fred Hutch staff for three-month positions to both write and edit content in the Biomedical Data Science Wiki, providing a stipend to support this work. Open to all; those interested can read more here and/or reach out to Justin Burge to apply.

• There’s a digital piano in the Coop Lab! There are also headphones if you’d like to keep your playing private, and some books of piano music. Please use it freely and treat it nicely! If you don’t use headphones, we recommend shutting the Coop Lab doors to keep from disturbing local offices.

• Coming soon: Wiki Docathon. Plans are in the works for a “docathon” (i.e., a hackathon for creating documentation) to add more content to the SciWiki. All skill levels will be welcome - for Git beginners, it will be a great opportunity to learn how to use GitHub in a friendly setting! More details to come; tentatively this event will be in April.

• TDS Faculty Recruit Visit: Golnaz Vahedi, PhD will give a chalk talk on Tuesday Mar 17 at 11 am in Sze East.

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link):

  • Register now: 

    • Intro to Git and GitHub begins March 10

    • Concepts in Machine Learning and Intermediate R: Machine Learning begin the week of March 16

  • Indicate interest in Hutch Learning to be notified: Sessions of Intro R and Intro Python will begin in late March or early April

  • Complete this form to be notified: Carpentries Instructor Training will be held in April or May and taught over two consecutive days. 

Latest Coop blog posts

• Overview of Community Groups

• Results of the Coop Customer Survey

• Highlights from rstudio::conf 2020

• Get flowing with Nextflow

• Submit your application for funding to take an online training course of your choosing!

• See more at https://fredhutch.github.io/coop/

February 2020 Coop News

News Items & Events

• Note: Today’s Coop Monthly Meeting is canceled and will return next month. 

• Coop professional development awards for online training: Need to learn a new programming language? Hear about a great online course you’d like to try? Submit an application for the Coop’s professional development awards for online computational training to pay for a short-term subscription to an online course provider. Find more information here.

• Register Now for Bioinformatics Workflow Manager Training with Nextflow, April 23-24: Are you a scientist who has to wrestle with computational pipelines to get your work done? You might be interested in learning more about Nextflow the workflow management tool for bioinformatics! Workflow management tools like Nextflow are free, open source software that make it easier to run your computational pipelines. Scientists at Fred Hutch are using workflow managers (Nextflow, Cromwell, etc.) to help with their work and now the TDS IRC with support from the Fred Hutch Microbiome Research Initiative is sponsoring training. Apply now for training at https://www.surveymonkey.com/r/8DT7FBR. There is no cost to attend, but space is limited. Applications will be open until February 21, and final acceptances will be sent out by March 6.

• SLU Collaborative Seminar Series: Single Cell Genomics. Join experts from UW Medicine, Allen Institute, and Fred Hutch for a conversation. Feb 24, 4:30-6:30 at Orin Smith Auditorium, UW Medicine

• Did you miss it? The Coop and TDS IRC hosted the WiDS meetup group in January, featuring Dora Dong, data scientist for HDC; Gretchen Krenn, program manager for Hutch Data Visualization; and Jenny Smith, Bioinformatics Analyst in CRD. Talk Recording: https://bluejeans.com/s/hdYLG/  

• Accepting Applications for SciWiki Writer-Editor Program: the program engages Fred Hutch staff for three-month positions to both write and edit content in the Biomedical Data Science Wiki, providing a stipend to support this work. Open to all; those interested can read more here and/or reach out to Justin Burge to apply.

• TDS Faculty Recruit Visits in February:

  • Jason Sheltzer, Seminar Feb 11, noon to 1pm in Pelton.  Chalk Talk 1:30pm in M1-A305/307 

  • Meghan Driscoll, Seminar Feb 14, 2-3pm in Pelton.  Chalk Talk 3:30 in M1-A303 [Seminar Link]

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link):

  • Sessions of Intro to R and Intro to Python are beginning next week!

  • Intro to Git and GitHub will be offered again in March.

  • Intermediate R: Machine Learning will be pilot tested in March. 

Latest Coop blog posts

• Making the most of Slack

• An introduction to the Coop Communities Slack for new members

• Welcome to the URSSI

• December 2019 Coop Panel Summary: Reproducibility in data-intensive science

• The Coop in Review: 2019

• See more at https://fredhutch.github.io/coop/

Job opportunities

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

January 2020 Coop News

News Items & Events

• TODAY: The Coop Monthly Meeting: 2020 Strategy Session. 12-1 pm in D1-080 (Sze West: not the Coop Lab). 

• Beer Chat Hosted by TDS IRC: Friday Jan 10, 5-7 pm in Weintraub Atrium.

• Women in Data Science Meetup:The Coop and TDS IRC are hosting the WiDS meetup group, featuring three speakers from the Hutch. Jan 15, 6-8 pm in D1-080/084 (Sze combo). Speakers: Dora Dong, data scientist for HDC; Gretchen Krenn, program manager for Hutch Data Visualization; and Jenny Smith, Bioinformatics Analyst in CRD.

• Second-generation interactive shell tools with Erick Matsen: Friday Jan 17, 11-12 pm in the Coop Lab(M1-B406). We’ll be discussing http://erick.matsen.org/2020/01/04/2nd-gen-interactive-shell.htm 

  • rather than naked shell, try tmux for an organized collection of shells
  • rather than local file system navigation, try fzf to fuzzily find what you want
  • rather than cd, try autojump, which remembers your favorite locations
  • rather than find, try fd, which has a much cleaner interface
  • rather than grep, try ag, which is simpler and faster

• TDS IRC Seminar: "Characterization of lineage decisions in single-cell developmental trajectories" Manu Setty, PhD, Jan 17, 10-11 am in Pelton. There will also be a Chalk Talk from 11:30-12:30 in M1-A305/A307. 

• Coop/TDS IRC Seminar: “The bounty of the commons: machine learning from everybody else's data” with Casey Greene, PhD. Jan 21, 1:30-2:30 pm in Pelton. There are now millions of publicly available transcriptomic profiles, which collectively represent a multi-billion dollar resource. The Greene lab is developing integrative machine learning approaches that take advantage of these public data to better understand datasets specific to a disease. Interested in meeting with Casey? Email carly@fredhutch.org.

• TDS IRC Seminar: “Global, organism-scale views of cell state heterogeneity and dynamics via novel single cell profiling techniques” with Junyue Cao, PhD, Jan 24, 10-11 am in Pelton. There will also be a Chalk Talk from 11:30-12:30 in D1-084 (Sze East).

• Accepting Applications for SciWiki Writer-Editor Program: the program engages Fred Hutch staff for three-month positions to both write and edit content in the Biomedical Data Science Wiki, providing a stipend to support this work. Open to all; those interested can read more here and/or reach out to Justin Burge to apply.

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for current courses though Hutch Learning (Hutch internal link). 

  • Register now for January’s concurrently taught sections of Concepts in Machine Learning and Intermediate Python: Machine Learning! This Concepts course is a pre- (or co-) requisite for a new course, Intermediate R: Machine Learning that will be pilot tested in March. 

  • Intro to R, Intro to Python, and Intro to Git/GitHub will also be taught in first quarter 2020. 

Job opportunities

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

December 2019 Coop News

Special announcement: We are excited to present the Coop Blog! We’ll be using the Coop Blog as a way to share information about community resources, highlight interesting solutions to technical problems in data science, adn describe data-intensive research at the Hutch. Have something to say to the Coop community? Respond to this email with your idea for a post, or file an issue in our GitHub repository.

News Items & Events

• TODAY: The Coop Monthly Meeting: Reproducibility in data analysis. Join us for a panel discussion featuring Hutch staff with a variety of perspectives on reproducibility: 12-1 pm in D1-080 (Sze West: not the Coop Lab). The Coop monthly meetings rotate among community meetings, panel discussions, and seminars, and are open to all.

• Request for Proposals: AWS Cloud Grants. TDS IRC and HDC are requesting applications from Fred Hutch researchers for AWS Cloud credits and engineering support to advance their data-intensive work. More information is available here (internal to Fred Hutch). There will be an information session on Tuesday December 10, 11-12 pm in the Coop Lab (M1-B406). The deadline for proposals is Monday, December 23. 

• Python Coding Group: Fri. Dec 6th 12-1 pm session - “Chat about Defensive Programming & Development Security” presented by Mike Nescot, Senior Information Security Architect, Hutch Data Commonwealth.

• Coop Seminar: “JupyterLab: the next-generation interface for Jupyter Notebooks”. Zach Sailer, PhD. Tuesday December 10, 12-1 pm in Behnke (M1-A303*). Zach will demonstrate the many features inside and around JupyterLab and explore the rich ecosystem of JupyterLab plugins developed by the open-source community. All are welcome! (*Note this is NOT in the Coop Lab) 

• TDS IRC Seminar: "Resiliency and Sensitivity of the 3D Genome Organization in T Cells" Tuesday December 10, 1:30 - 2:30 pm in Pelton Auditorium. Golnaz Vahedi, PhD Assistant Professor of Genetics, University of Pennsylvania School of Medicine.

• BioStats/TDS Seminar: “Veridical Data Science” with Bin Yu, Ph.D - Wednesday December 11, 12-1pm in M1-A305/307. Overview of a framework for veridical data science comprised of both workflow and documentation and aimed at providing reproducible transparent results across the data science life cycle.

• GitHub Enterprise Overview: Monday December 16, 12-1 pm in Yale J3-102. GitHub Enterprise staff will share new features and happenings highlighted here: https://github.blog/. Sponsored by Scientific Computing and open to all!

• Mark your calendars: Women in Data Science Meetup at the Hutch! The Coop and TDS IRC are hosting the WiDS meetup group, featuring three speakers from the Hutch. January 15, 6-8 pm in D1-080/084 (Sze combo). Speakers: Dora Dong, data scientist for HDC; Gretchen Krenn, program manager for Hutch Data Visualization; and Jenny Smith, Bioinformatics Analyst in CRD.

• Accepting Applications for SciWiki Writer-Editor Program: the program engages Fred Hutch staff for three-month positions to both write and edit content in the Biomedical Data Science Wiki, providing a stipend to support this work. Open to all; those interested can read more here and/or reach out to Justin Burge to apply.

Upcoming Trainings

• JupyterLab Workshop: “Deploying JupyterLab here, there, and everywhere” led by Zach Sailer, PhD. December 11, 11 am - 12 pm in Coop Lab (M1-B406). Interested in learning how to use Jupyter notebooks?  In this workshop, we’ll get you programming interactively with JupyterLab immediately. All are welcome!

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for current courses though Hutch Learning (Hutch internal link). We’ll begin listing courses soon for January through March, including Intro to Python, Intro to R, Concepts in Machine Learning, Intermediate Python: Machine Learning and Intermediate R: Machine Learning.

• Intro to R for SAS users: fredhutch.io is offering a special session of Introduction to R for current SAS users on Dec 9, 10, 16, and 17 from 9-11 am in the Coop Lab (M1-B406, Arnold). We’ll be covering material similar to the fredhutch.io Introduction to R class (course description available here, and course materials here), with a goal of helping you identify some of the key differences between SAS and R, and how R coding can provide more flexibility in your current data manipulation and visualization tasks. Register using this form.

Job opportunities

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

• Assistant/Associate Member Faculty Position, computational Biology and Biomedical Data Science, in the TDS IRC: Job Opening

November 2019 Coop News

News Items & Events

• Coop Anniversary Party next week - Join us Wednesday November 13 to celebrate a great first year for the Coop. Food, drinks, and feedback boards will be in Arnold Atrium from 3-5 pm and all are welcome. Come for the food and drink; stay for the networking!
  
  

• SLU Collaborative - Big Data Collaboration: Methods, Technology Development & Data Sharing. Monday November 18 in Pelton Auditorium, 4-6 pm. The SLU Collaborative is a joint effort to share knowledge across the Hutch, Allen Institute, and UW. This event will be a panel discussion of cross-institutional collaborations involving big data. Panelists: Lydia Ng, PhD, Senior Director of Technology, Allen Institute; William Stafford Noble, professor, Genome Sciences, University of Washington; Michael Zager, Director of the Center for Data Visualization, Fred Hutch. Questions? Interested in presenting a poster? Email SLUCollab@fredhutch.org

• UW Data Science Seminar - Wondering how to work better as a lab group? Julia Stewart Lowndes will speak on "R and friends for better science in less time in big (and small) team collaborations" November 19 from 4:30-5:30 pm at UW in Physics/Astronomy Building Room 118. 

• Python Coding group - We are happy to have Erick Matsen hold another interactive event on Friday November 22 from 12-1 pm in Coop Lab (M1-B406) in which we’ll build a Docker image containing conda, and then test it using Travis. Everyone should have Docker installed ahead of time and make accounts at quay.io and travis CI. Ping @Justin Burge on Slack if you get stuck with any of the installs. This tutorial will use conda (and thus is Python-related) but the event is open to all.

• Software Design Group - note date changed from normal schedule: Come Monday November 25 from 12-1 pm in Coop Lab (M1-B406) to talk about EasyBuild with our own HPC System Engineer John Dey. All are welcome!

• The Coop Monthly Meeting - Reproducibility in data analysis. Join us for a panel discussion Tuesday December 3 from 12-1 pm in Coop Lab (M1-B406). The Coop monthly meetings rotate among community meetings, panel discussions, and seminars, and are open to all.

• Coop Seminar on Project Jupyter - Come Tuesday December 10 from 12-1pm in Behnke (M1-A303*) to hear special guest Zach Sailer from Project Jupyter give a seminar on an overview of Project Jupyter. All are welcome! (*Note this is NOT in the Coop Lab)

• Jupyter Workshop - Interested in learning how to use Jupyter notebooks? Join us on Wednesday December 11 from 11am-12 pm in Coop Lab (M1-B406) for a workshop from Zach Sailer from Project Jupyter. All are welcome!

• Accepting Applications for SciWiki Writer-Editor Program - the program engages current staff from each of the Divisions for three-month positions to both write and edit content in the Biomedical Data Science Wiki, providing a stipend to support this work. Open to any and all, those interested can read more here and/or reach out to Justin Burge jburge@fredhutch.org to apply.

• TDS IRC Retreat Survey - If you attended the Translational Data Science retreat on October 7, please fill out this brief survey to share what went well and what can be done to improve the program: https://redcap.iths.org/surveys/?s=JMWH7KCYFM

Job opportunities

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

• Assistant/Associate Member Faculty Position, computational Biology and Biomedical Data Science, in the TDS IRC: Job Opening

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for current courses though Hutch Learning (Hutch internal link). We’ll start listing courses for early 2020 in December.

• Intermediate Python: Machine Learning: fredhutch.io is pilot testing a new course in November! Thomas Adams will be teaching a technical skills course, Intermediate Python: Machine Learning, which has a prerequisite of Introduction to Python (or equivalent knowledge). This course will be offered again in early 2020.

• November Tech Exchange: This month’s topic will be Microsoft Teams, a modern communication and collaboration platform available to all staff, on Tuesday, November 19 from 12-1pm in Arnold M1-A303. No registration is required; snacks and drinks will be provided. Please contact Robert McDermott with any questions. Sponsored by the Technology Exchange Community Group .

 

October 2019 Coop News

News Items & Events

• October is Data Science Month! TDS IRC, fredhutch.io, HDC, Biostats, and others are all contributing events and effort to the Hutch’s first Data Science Month. See a full list of events on CenterNet (internal only). For those outside of the Hutch all events are on the Coop Google Calendar. Here is a flyer that is accessible to all of the various events taking place.

• Coop Anniversary Party: Mark your calendars for Wednesday, November 13! We are celebrating a great first year for the Coop from 3-5 pm. Food, drinks, and feedback boards will be in the Arnold Atrium. All are welcome!

• Welcome Justin Burge! Justin is the newest member of the team that works on The Coop, fredhutch.io, and HDC. He joins us from Communications & Marketing here at the Hutch and will be helping with community building, coordination, and training.

Job opportunities

• Scientific Liaison for Hutch Data Commonwealh: Job opening

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

• Assistant/Associate Member Faculty Position, computational Biology and Biomedical Data Science, in the TDS IRC: Job Opening

 

Upcoming Trainings

• fredhutch.io offers free short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills (like R or python coding) for research purposes. Fred Hutch and SCCA employees can view and register for current courses though Hutch Learning (Hutch internal link).

• October Tech Exchange: October’s topic will be Docker, a tool used to create and deploy applications using containers. Tuesday, October 22 from 12-1pm in Arnold M1-A303. This talk is targeted at IT and administrative professionals. No registration is required; snacks and drinks will be provided. 

• Tableau Desktop Fundamentals I & II (Accelerated): Registration is now open for Hutch Tableau users for a hands on, accelerated training on Tableau. This three-day training from a Tableau instructor will teach you to build complex calculations and better dashboards. Register your interest now to secure one of 20 spots. Contact Jasmine Hwang (jhwang2@scharp.org).

 

September 2019 Coop News

News Items & Events

• TODAY: Coop Community Meeting, 12-1 in M1-A303 (Behnke Suites). Please join us for the quarterly Coop Community Meeting! Special guests from SCHARP, the data science group at SCCA, and the HutchBASE development group from HDC will present on their work. We will also have time for general announcements, questions, and ideas. 

• Technical blog: We’re thinking about creating an externally facing technical blog to share the biomedical research applications of our work across the center in data science, software and data engineering, statistics, computational biology, etc.with a broader audience. If you have any interest in contributing content or guiding format, please contact Emily Silgard at esilgard@fredhutch.org.

• Data management at the Hutch: Based on our August focused on data management, we are working on improving wiki documentation about data management, as well as creating a new course called “Data for Data Science”. Keep an eye out for an opportunity to participate in the pilot of this course! 

• protocols.io founder Lenny Teytelman presented in August on protocols.io, a platform makes it easy to share research recipes and to collaborate on method development, both publicly and privately. You can view the talk here.

• Shiny application group: Our latest community group is focused on developing and maintaining Shiny applications. Shiny is a package in R that allows development of interactive web applications for data analysis. Join fellow researchers and developers on the third Monday of the month from 12-1pm in the Coop Lab (M1-B406, Arnold). See the #r-user-comm channel on The Coop Communities Slack for more information.

• Python package development: The Python coding group will have a topic discussion on development and maintenance of Python packages on Friday, September 6 from 12-1pm in the Coop Lab (M1-B406, Arnold). See the #python-user-comm channel on The Coop Communities Slack for more information.

• Software Development group topic: GitHub and collaboration. The topic for this month's Software Development group (formerly known as Software Design group) will be collaboration using GitHub. We'll be discussing forking vs branching for collaboration, different approaches to branches (master, gh-pages, development branches, feature branches), and other topics that will help advance your skills beyond the basic git workflow (add, commit, branch, merge). This group is open to all folks interested in GitHub as a tool! See the #software-engineers channel on The Coop Communities Slack for more information.

• Skill share: Trelliscope. Trelliscope is a plotting method that allows interactive visualization of plots from different groups of data. Ryan Hafen will be visiting campus on Monday, September 23 from 12-1pm in the Coop Lab (M1-B406, Arnold) to present on trelliscopejs, an R package designed to implement this data visualization approach. All are welcome to join in this discussion!

• Announcing Skill Shares: Skill Shares are short (~1 hour), single-occurence sessions that provide a brief introduction to a concept, package/library, or tool. We are intending these sessions to be a more lightweight option to learning than courses, as they are taught by volunteers from our community (or visitors to campus), scheduled on an ad hoc basis, and usually held in the Coop Lab. While we’ll attempt to list these in the newsletter, pop-up sessions might be scheduled only a few weeks or days in advance, so watch our calendars and Slack for more information. 

Job opportunities

• Hutch Data Commonwealth, Coop, and fredhutch.io are hiring a training specialist. Come help us make the Hutch more data-savvy! Job opening
  

• SCCA is hiring a Data Scientist to join the Advanced Analytics team: Job opening

• Hutch Data Commonwealth is hiring a Data Scientist II: Job opening

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

• Assistant/Associate Member Faculty Position, computational Biology and Biomedical Data Science, in the TDS IRC: Job Opening

 

Upcoming Trainings

• fredhutch.io offers short courses in reproducible computational research methods. These courses are most appropriate for researchers who are interested in learning computing skills for research purposes. Current courses include Intro to R, Intro to Python, Intermediate Python: Programming, and Intro to Git/GitHub. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning(Hutch internal link). These courses are most appropriate for researchers who are interested in learning computing skills for research purposes. For questions about these courses, or if you are interested in assisting with teaching a course, please contact khertwec@fredhutch.org.

• Upcoming fredhutch.io courses: We will be pilot testing the following new courses over the next few months: Data for Data Science and Concepts in Machine Learning with be tested in October, and Intermediate Python: Machine Learning will occur in November. More information and registration will be available in Hutch Learning in mid-September. These classes will be added to our continued course scheduling in 2020.

•  

August 2019 Coop News

News Items & Events

• TODAY 12-1: How do you store and share data? Come talk data management at the Hutch: The August monthly meeting for the Coop will be focused on data management. Come to the Coop Lab (M1-B406) today at 12 pm with questions and concerns! Do you have questions about the best way to store data? Are you confused about how to share data with other labs at the Hutch, or outside collaborators? We are developing recommendations for managing data and need to know how you currently approach these issues! 

• Tues Aug 13: Coop seminar in collaboration with the Arnold Library. For reproducibility, we need the methods behind the data. protocols.io founder Lenny Teytelman will present on a platform makes it easy to share research recipes and to collaborate on method development, both publicly and privately. Fred Hutch PI Steve Henikoff will join to share his experiences with the platform. August 13, 10-11 am in Arnold - M1-A303. Please attend if you are able, but you can stream the talk here (during the event or afterwards)

• Protocols.io institutional subscription: The Arnold Library has teamed up with the Coop and Research Administration to introduce a new institutional subscription to protocols.io. This is an open source collaborative platform and preprint server for research methods, computational or operational workflows, and other protocols with the goal of increasing research reproducibility, transparency, and accessibility. The subscription grants all Fred Hutch users access at the premium level, with tools for managing group collaboration. Contact the Library at library@fredhutch.org with any questions.

• It’s summer: The Coop is going outside! We are establishing a web presence external to Fred Hutch and the CenterNet pages. Content will be migrating to http://thecoop.fredhutch.org  and CenterNet will be used for Hutch-specific communication.

• Python coding group: Join fellow researchers and developers every Friday from noon to 1 pm in the Coop Lab (M1-B406, Arnold) for the newest of our community coding groups! This group discusses methods of programming in Python and is open to participants bring code of their own to troubleshoot. Python coders of all levels of expertise are welcome. See the #python-user-comm channel on The Coop Communities Slack for more information.

• Submit  an abstract for the Translational Data Science Integrated Research Center Retreat: Postdocs and graduate students from TDS & CCSG BioStats and CompBio Members and BBE & Computational Biology trainees are invited to submit an abstract for a lightning talk and/or poster to be presented at the TDS IRC retreat on October 7. Priority will be given to research projects highlighting the use of computational approaches and/or the generation of unique data types needing new approaches for analysis and visualization. Lightning talk submission due Aug 30; poster submission due Sep 15. Registration site: https://redcap.iths.org/surveys/?s=RXMNRJ7DEA.

Job opportunities

• Hutch Data Commonwealth, Coop, and fredhutch.io are hiring a training specialist. Come help us make the Hutch more data-savvy! Job opening

• SCCA is hiring a Data Scientist to join the Advanced Analytics team: Job opening

• Hutch Data Commonwealth is hiring a Data Scientist II: Job opening

• Data Scientist, Spatial Single-Cell RNA Sequencing in the Fred Hutch's Innovation Lab: Job opening

• Post-Doctoral Research Fellow, Data Science in the Gottardo Lab: Job opening

• Staff Scientist, Computational Biology in the Gottardo Lab: Job opening

• Research Tech II, Spatial Single-Cell RNA Sequencing in the Bielas Lab: Job opening

Upcoming Trainings

• Announcing Tech Exchange: This group is an informal learning forum for employees in technology-focused jobs to share technical skills. Subscribe to the TechExchange mailing list for more information. This group is run by Center IT and is most appropriate for individuals who want to discuss the technical details of tools commonly used in positions focused on administration and infrastructure.

• August Tech Exchange: Introduction to Version Control with Git, hosted by Robert McDermott, Tuesday, August 20 12:00-1:00 in Arnold M1-A303. This talk is targeted at IT and administrative professionals with little or no previous experience using Git for version control, and will cover topics like: what is version control and why you need to learn it and using Visual Studio Code (free) to avoid the command-line. No registration is required; snacks and drinks will be provided. 

• Fredhutch.io offers short courses in reproducible computational research methods, which currently includes Intro to R, Intro to Python, Intermediate Python: Programming, and Intro to Git/GitHub. Fred Hutch and SCCA employees can view and register for courses though Hutch Learning (Hutch internal link). These courses are most appropriate for researchers who are interested in learning computing skills for research purposes. For questions about these courses, or if you are interested in assisting with teaching a course, please contact khertwec@fredhutch.org.

• UCSC Genome Browser training: Bob Kuhn from UCSC will be leading this training on using the UCSC Genome Browser on Friday, August 23 from 9 am to noon in M1-A305. Topics covered include: features and navigation in the Genome Browser, types of data to visualize, and advanced features of the browser. Reserve a space in this course by completing this form (note: there is limited space available for researchers from other academic institutions). Contact khertwec@fredhutch.org with any questions.

Alert: Newsletters below this line may have links that are internal to Fred Hutch

July 2019 Coop News

News Items & Events

• July Coop Meeting/Happy Hour: July 11th (Thursday) from 4-6 PM in the Weintraub Cafeteria the Coop is having a beer social! Come and meet other people working on similar projects and let’s build community! We will also be celebrating the launch of the new Fred Hutch Discovery search tool that allows you to search for files in Hutch storage systems. 
• Overview of User Experience (UX) research: The Software Design lunch group on Monday, July 8 from noon-1pm will be hosting a special session on user experience research. Paige Nuzzolillo from Delta Dental will be speaking on  “Getting to Know Our Users: Curiosity, Empathy, Listening, Learning and Experimentation,” and Helen Miller (Gottardo Lab) will give a demo of ImmuneScape and overview the usability testing implemented in its design. 
• Protocols.io overview: Interested in making your research more reproducible? Care about open science? Join a discussion of protocols.io with the tool founder Lenny Teytelman and Fred Hutch PI Steve Henikoff. August 13, 10-11 am (location M: Arnold - M1-A303).

Funding Opportunities

• Essential Open Source Software for Science
  https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/
  The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research. Applicants can request funding between $50k and $250k for one year. This RFA is the first of a series. CZI will invite applications during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020. Read our Medium post to learn more.

Job opportunities

• Hutch Data Commonwealth is hiring an Engagement Manager (grad degree required): Job opening
• The Translational Data Science Integrated Research Center (TDS IRC) is hiring a staff data scientist: Job opening
• SCCA is hiring a Data Scientist to join the Advanced Analytics team: Job opening
• Hutch Data Commonwealth is hiring a Data Scientist II: Job opening
• Data Scientist III, Spatial Single-Cell RNA Seq: Job opening
• Research Technician II, Spatial Single-Cell RNA Seq: Job opening

Upcoming Trainings

• UCSC Genome Browser training: Bob Kuhn from UCSC will be leading this training on using the UCSC Genome Browser on Friday, August 23 from 9 am to noon in M1-A305. Topics covered include: features and navigation in the Genome Browser, types of data to visualize, and advanced features of the browser. Fred Hutch employees will be able to register for the course though Hutch Learning in mid-July. Contact khertwec at fredhutch.org with any questions.
• Fredhutch.io offers short courses in reproducible computational research methods. We are moving to a system of scheduling classes by quarter (in three-month segments); sessions for July, August, and September will be posted in the next few weeks. Fred Hutch employees can view and register for courses though Hutch Learning. For questions about these courses, or If you are interested in assisting with teaching a course, please contact Kate (khertwec at fredhutch.org).
• Office hours for fredhutch.io are Tuesday from 9am to noon in the Coop Lab (Arnold M1-B406). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!

June 2019 Coop News

News Items & Events

• TODAY: Coop Community Meeting (Tuesday June 4th, 12-1PM M1-A303). The Coop monthly meeting for June is a community meeting for you to get updates from data science colleagues at the Hutch and learn more about the tools and resources available to you. Please join us to learn more about groups holding office hours and the services they can provide, see a demo of Discovery (the file system search tool currently in development in Hutch Data Commonwealth), and hear reports about other data science projects at HDC.

• Cascadia R Conference tickets for June 8 are still available at cascadarconf.com. The conference is focusing on highlighting the ways R is being used across our region and is a great way to meet other R users.

• Dr. Oren Etzioni: On Tuesday, June 18th at 1:30 PM as a part of the TDS Seminar Series, Matthew Trunnell is hosting.

• MATLAB parallel computing: MATLAB representatives will be giving a lunchtime presentation on June 25 on using MATLAB for parallel computing and how to run jobs on the Hutch’s local computer cluster. Watch the Coop calendars for more information!

• Have stuff? Want help finding it? HDC is launching its new search tool, Discovery. Discovery allows you to search for your stuff in the Hutch's Fast, Economy local (Swift), and Economy cloud (AWS S3) storage systems. This tool is currently in development. Please try it out at https://discovery.fredhutch.org/ and let us know how we can improve it. Please send feedback to bret at fredhutch.org

• Have a community you would like to foster? Helping to organize a monthly or weekly discussion group is a great way to get to know the community and gain some leadership experience. Send an email to coophelp at fredhutch.org, or jump on Slack and start a conversation.

• Using the Coop Lab: We have put some guidelines up on CenterNet about using the Coop Lab.

• New resources in the Coop Lab: If you visit our shared workspace in M1-B406, feel free to take advantage of two new resources available to you. First, we have an anonymous comment box available for you to leave questions or concerns about our events or suggestions for us to improve the community. Second, we have created two bulletin boards: “Data Science Things I Want/Need” (such as a mentor in a specific area, or someone experience with a particular type of analysis) and “Things I have to Share” (such as a willingness to mentor in a particular area).

• July Coop Meeting: Details are still in the works, but in July we will be having a beer social. Come and talk about code, learn in a relaxed setting what others are working on, and get to know your fellow data enthusiasts. All are welcome to join! Be on the lookout for updates!

Job opportunities

• IIRC is hiring a Director for the Advanced Technology Lab: Job opening

• The Translational Data Science Integrated Research Center (TDS IRC) is hiring a staff data scientist: Job opening

Upcoming Trainings

• Fredhutch.io offers short courses in reproducible computational research methods, and coordinates with invited instructors to teach special topics. Fred Hutch employees can view and register for courses though Hutch Learning. For questions about these courses, or If you are interested in trying out teaching, please contact Kate (khertwec at fredhutch.org).

• Carpentries Instructor Training: The Hutch will be hosting Instructor Training on June 20-21 for the The Carpentries, a non-profit that teaches computational and data skills to researchers around the world. If you are interested in developing your teaching skills, please email Kate (khertwec at fredhutch.org) to reserve one of the few remaining seats.

• Office hours for fredhutch.io are Tuesday from 9am to noon in the Coop Lab (Arnold M1-B406). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!

May 2019 Coop News

News Items & Events

• TODAY: Bioinformatics & Cloud Computing with Reproducible Workflows. Sam Minot, PhD will go over Nextflow and how scientists can use it to analyze their own data in the AWS cloud, with particular attention paid to the practicalities of computing at Fred Hutch. CenterNet Event - Tuesday May 7th, 12-1PM M1-A303. Please attend in-person if you are able, but there is a live-stream available for those who cannot.
  
  
• TDS IRC Guest Speaker: Bayesian Methods for Studying Tumour Heterogeneity. Andrew Roth, PhD will present Wednesday May 8th, 2019 2-3 PM in Pelton Auditorium.
  
  
• TDS IRC Guest Speaker: Modeling Cancer Evolution at Single Cell Resolution: Challenges and Opportunities. Sohrab Shah, PhD will present Monday May 13th, 2019 2-3 PM in Pelton Auditorium.
  
  
• ROpenSci representatives will be giving short talks and facilitating discussion about their project on Wednesday, May 22 from 1-2 PM in The Coop Lab (M1-B406). Come learn about the resources they have to offer to the R community, as well as how you can get involved in open source software projects!
  
  
• SciComp Office Hours- Now with Data Science and Data Engineering: HDC data scientists and data engineers will be joining the SciComp crew for office hours in the Coop Lab (M1-B406) Wednesdays, 10 AM - 12 PM
  
  
• Ethics/Compliance/Security Office hours - Now on Wednesdays 10:00 to 11:30 in the Coop Lab (M1-B406). Need to know if you are using your data ethically? Is your data is secure? Do you know what you need to know to satisfy applicable data use requirements? ISO and HDC Compliance are providing some Privacy, Ethics and Compliance – “P.E.C”-ing orders support.
  
  
• Seattle UseR Meetup Group will be meeting Thursday, May 16th, for an evening of lightning talks in Behnke Suites (M1-A307) from 6-8pm. RSVP here and sign up to give a lightning talk here!
  
  
• Cascadia R Conference tickets are still available at cascadarconf.com. The conference is focusing on highlighting the ways R is being used across our region and is a great way to meet other R users.
  
  
• Have stuff? Want help finding it? HDC is launching its new search tool, Discovery. Discovery allows you to search for your stuff in the Hutch's Fast, Economy local (Swift), and Economy cloud (AWS S3) storage systems. This tool is currently in development. Please try it out at https://discovery.fredhutch.org/ and let us know how we can improve it. Please send feedback to bret at fredhutch.org
  
  
• Have a community you would like to foster? Helping to organize a monthly or weekly discussion group is a great way to get to know the community and gain some leadership experience. Send an email to coophelp at fredhutch.org, or jump on Slack and start a conversation.

Job opportunities

• HDC is hiring a Research Data Specialist: Job opening. Email carly at fredhutch.org with questions!
  
  
• IIRC is hiring a Director for the Advanced Technology Lab: Job opening
  
  
• The Translational Data Science Integrated Research Center (TDS IRC) is hiring a staff data scientist: Job opening

Upcoming Trainings

• Short courses in reproducible computational research methods are available through fredhutch.io. Fred Hutch employees can view and register for courses though Hutch Learning. In addition to introductory courses in R, Python, and Git/GitHub, we are pilot testing materials for an intermediate Python course focusing on programming. For questions about these courses, or If you are interested in trying out teaching, please contact Kate.
  
  
• Office hours for fredhutch.io are Tuesday from 9am to noon in the Coop Lab (Arnold M1-B406). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch! 

April 2019 Coop News

News Items & Events

• TODAY: Panel on Ethics in Data Science: The Coop will host experts to discuss Ethics on April 2 from 12-1 pm in M1-A303 (CenterNet event). We have a great group of panelists and want your questions!

• Tidy Tuesday, now called Data Viz Group:  To avoid confusion, the Tidy Tuesday Group is now listed on calendars as the Data Viz Group. This group meets every Wednesday at noon in The Coop Lab to create visualizations of the weekly dataset selected by R for Data Science.

• FHBig Blog: Do you have a helpful tip, technical discovery, or other information about data science and bioinformatics you’d like to share with our community? Consider submitting a blog post! Instructions for submission are here.

• The Northwest Data Science Summit, May 7th-8th at UW: a jointly-sponsored event hosted at the UW eScience Institute and the University of British Columbia (UBC) Data Science Institute This event will feature talks from data science experts, networking opportunities, lightning talks, a poster session, and more! Register here.

• TDS Seminar Tuesday April 16th, Pelton Auditorium 1:30-2:30 PM: Sam Minot, PHD: Staff Scientist Fredricks Lab, VIDD - High-dimensional clustering of microbial genes identifies reproducible associations of the microbiome with colorectal cancer

• Shwetak Patel Talk rescheduled: Originally set to occur on February 21st and later cancelled, this talk will now be Wednesday, June 26, 2019 in M1-A305/307. This talk is Hosted by Biostatistics and DSAG.

• Coop Lab use: Interested in using Coop Lab for co-working, office hours, etc? We are working out how the space will be managed and hope to have info on CenterNet soon. Email coophelp at fredhutch.org if you have questions that require a response in the interim.

• SciComp Office Hours- Now with Data Science and Data Engineering: HDC data scientists and data engineers will be joining the SciComp crew for office hours in the Coop Lab Wednesdays (10:00AM - 12:00PM)

• Fred Hutch Biomedical Data Science Wiki is looking for additional Wiki Writer/Editors.   Ideally these Editors would be engaged in ongoing research and who use (or would like to use), some of the Fred Hutch supported high performance computing infrastructure (rhino/gizmo and beyond) to help with reviewing content provided by IT.  This is a relatively small (~3-4 hrs/week) time commitment, there is a stipend available and so much learning potential to hear directly from IT how to use cool new resources for your work. See the page on the Writer/Editor program here for more information: or email Amy Paguirigan at apaguiri at fredhutch.org if you’re interested. Note: you must be a Fred Hutch employee to receive the stipend.

• Software Design Group meets every second Monday of the month at noon. If you’re writing code for research, please consider joining us for code review and sharing ideas for improving software design. All programming languages welcome!

• Have a community you would like to foster? Send an email to coophelp at fredhutch.org, or jump on Slack and start a conversation.

Funding opportunities

• Joint IRC Pilot Award for New Technology & Data Analysis proposals due Apr 26: Early stage pilot funding is available for projects that use new technologies to generate large and complex data sets in immunotherapy and pathogen-associated malignancies.  Application details and budget worksheet are on CenterNet here.  Questions may be directed to Sheila Charles, scharles at fredhutch.org.

Job opportunities

• IIRC is hiring a Director for the Advanced Technology Lab: Job opening

• The Translational Data Science Integrated Research Center (TDS IRC) is hiring a staff data scientist: Job opening

Upcoming Trainings

• Current fredhutch.io course offerings include Intro to R, Intro to Python, and Intro to Git and GitHub. New courses in development and undergoing pilot testing include Data Management with Spreadsheets, Programming with Python, and additional intermediate courses in R. Watch Hutch Learning for scheduling of these and additional courses under development starting in 2019. If you are interested in trying out teaching, please contact Kate to talk about opportunities.

• Office hours for fredhutch.io are Tuesday from 9am to noon in M1-B406 (Arnold). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!

March 2019 Coop News

News Items & Events

• Community Meeting featuring Matthew Trunnell (Chief Data Officer): Our first Coop community meeting of 2019 will be Today from 12-1 PM in The Coop Lab, M1-B406. Matthew Trunnell will be answering questions and providing info about data science at Fred Hutch. We will also have general community updates and time for questions and announcements. (Originally Raphael Gottardo was scheduled to speak but had a conflict).

• Coop Lab: The new space is open! M1-B406 (Arnold) has been converted into a classroom, co-working, and small group meeting space for computational work called Coop Lab. SciComp has moved their Wednesday Office Hours into the Coop Lab; we hope to be moving more office hours to that location, so please watch the locations of office hours as they may change.

• Coop Lab use: Interested in using Coop Lab for co-working, office hours, etc? We are working out how the space will be managed and hope to have info on CenterNet soon. Email coophelp at fredhutch.org if you have questions that require a response in the interim.

• Data Science Seminar: Dr. Kevin Jamieson from UW will speak on March 19 from 1:30-2:30 in Pelton Auditorium. Talk title:  “Collecting Data More Efficiently with Data-driven Sequential Experimental Design.”

• Panel on Ethics in Data Science: The Coop will host experts to discuss Ethics on April 2 from 12-1 pm in M1-A303 (CenterNet event). We have a great group of panelists and want your questions! Email coophelp at fredhutch.org with ideas for questions to ask the panel.

• New communities:
  • TidyTuesday Group (every Wednesday at noon in The Coop Lab): Join us each week to brainstorm and implement data visualization from data posted as a part of the R for Data Science (R4DS) TidyTuesday project. Even if R isn’t your prefered method of choice for data visualization, you’re still welcome to join!
  • Tableau Group: The Tableau user group held a kickoff meeting on February 25. If you’re interested in using this software for data visualization, keep an eye on their channel in The Coop Communities Slack.
  • Software Design Group (every second Monday of the month at noon, starting March 11): If you’re writing code for research, please consider joining us for code review and sharing ideas for improving software design. All programming languages welcome!
  • Have a community you would like to foster? Send an email to coophelp at fredhutch.org, or jump on Slack and start a conversation.

• Talk recording: Did you miss Os Keyes’s seminar “Trans/Formations: Data, Entropy, and Trans Lives”? Don’t worry! The talk was recorded and is available for viewing.

Funding opportunities

• Joint IRC Pilot Award for New Technology & Data Analysis proposals due Apr 26: Early stage pilot funding is available for projects that use new technologies to generate large and complex data sets in immunotherapy and pathogen-associated malignancies.  Application details and budget worksheet are on CenterNet here.  Questions may be directed to Sheila Charles, scharles at fredhutch.org.

• AWS Academic Program’s Machine Learning Research Awards: deadline March 24. This program funds eligible universities, faculty, PhD students and postdocs that are conducting novel research in machine learning. More information available from Amazon here.  Please let Kit Crafton know if there is interest from your lab! He is happy to coordinate or otherwise assist any interested submitters.

Job opportunities

• IIRC is hiring a Director for the Advanced Technology Lab: Job opening

• The Translational Data Science Integrated Research Center (TDS IRC) is hiring a staff data scientist: Job opening

Upcoming Trainings

• Current fredhutch.io course offerings include Intro to R, Intro to Python, and Intro to Git and GitHub. Watch Hutch Learning for scheduling of these and additional courses under development starting in 2019. If you are interested in trying out teaching, please contact Kate to talk about opportunities.

• Kate will be hosting office hours for fredhutch.io on Tuesdays from 9am to noon in M1-B406 (Arnold). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!

Feb 2019 Coop News

News Items & Events

• ** POSTPONED DUE TO WEATHER** Now 2/13/2019 in M1-A303
  First Speaker in New Data Science Seminar Series TODAY: Os Keyes. Os Keyes of UW is speaking at FH on February 5th from 12-1PM in B1-072/074 with a talk called “Trans/Formations: Data, Entropy, and Trans Lives”. Os will discuss considerations and implications of collecting demographic data and classifying transgender people.
  
  
• FHBig Monthly Meeting Thurs Feb 7, 1-2 PM in M4-A805-A817. Jason Underwood from Pacific Biosciences (PacBio) gives a talk about long-read SMRT-seq technology. Topics include when to use short-read or long-read technology, applications of SMRT-seq to cancer research, structural variant detection, novel isoform discovery and relevant papers using SMRT-seq.
  
  
• Coop Lab Open House: The new space is open! M1-B406 (Arnold) has been converted into a classroom, co-working, and small group meeting space for computational work called Coop Lab. We hope to move office hours into this space to become a one-stop shop! The Coop will host an Open House on Tuesday Feb 19  from 12 - 4 PM. Stop by to see the new space, have a snack, and say Hi.
  
  
• Seminar: Dr. Shwetak Patel (co-sponsored with Biostats seminar series) on February 21st in Thomas D1-080/084.  Dr. Patel is the Washington Research Foundation Entrepreneurship Endowed Professor in Computer Science and Engineering and Electrical Engineering at UW. His work includes developing new sensing systems, energy and water sensing, mobile health, and developing new interaction technologies.
  
  
• Community Meeting featuring Raphael Gottardo: Our first Coop community meeting of 2019 will be on March 5 from 12-1 PM tentatively in The Coop Lab, M1-B406. Raphael Gottardo will be providing an overview and answering questions about the new Translational Data Science Integrated Research Center (TDS IRC). We will also have general community updates and time for questions and announcements.

Funding opportunities

• TDS IRC Postdoctoral Fellowship Award Due Feb 28: The TDS IRC is offering funding for postdoctoral fellows in data science.  The ideal fellow will be a quantitative scientist with dual mentors in data science and translational research.  Priority will be given to fellows who create new collaborations across the Center. More information on the TDS IRC CenterNet Page.
  
  
• Joint IRC Pilot Award for New Technology & Data Analysis proposals due Apr 26: Early stage pilot funding is available for projects that use new technologies to generate large and complex data sets in immunotherapy and pathogen-associated malignancies.  Examples of new technologies include, but are not limited to, CITE-seq, ATTAC-seq, other single cell sequencing techniques, CyTOF, high dimensional flow cytometry, multi-spectral IHC, epigenomic analyses, and others.  Projects creating benchmark or reference data sets are encouraged. The IRCs will fund 4-5 awards of $75,000 direct costs. Application details and budget worksheet are on CenterNet here.  Questions may be directed to Sheila Charles.

Other Updates

• SciComp’s John Dey represented FH in Ghent at the 4th annual EasyBuild users Meeting and presented on how we build reproducible software at Fred Hutch. Watch the video here: https://youtu.be/f5DAEq5I4oI. Check out the full Fred Hutch Scientific Software Inventory: http://fredhutch.github.io/easybuild-life-sciences/

• Ellis Hughes from SCHARP is presenting Intro to R Package Development at the Seattle UseR meetup on Wednesday, February 6 at the SLU WeWork location. RSVP here.
  
  
•  Report from Software Carpentry Bootcamp: On January 22-25, fredhutch.io hosted the first Software Carpentry bootcamp at the Hutch. The materials on Unix programming for automation, Git version control, and programming in Python were well received and we are looking forward to continuing to teach similar materials in coming months.

Upcoming Trainings

• Current fredhutch.io course offerings include Intro to R, Intro to Python, and Intro to Git and GitHub. Watch Hutch Learning for scheduling of these and additional courses under development starting in 2019.
  
  
• Kate will be hosting office hours for fredhutch.io on Tuesdays from 9am to noon in M1-B153 (Arnold). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch.

Jan 2019 Coop News

General Updates

• Calendar of events: The Coop’s role is to unite efforts - that means making sure everyone knows about trainings, seminars, hackathons, and other data science and bioinformatics activities. To help with this, we maintain the Coop calendar in three formats. Choose what’s best for you:

  • Google (administered by FHBig)

  • Outlook: Search for “The Coop Email” under “Add Calendar from Directory”

  • CenterNet (internal to Fred Hutch): Select “The Coop Bioinformatics and Data Science Interest Group” from the “Host” dropdown

• Working and training space: Work is underway to convert M1-B406 (Arnold) into a classroom, co-working, and small group meeting space for computational work called Coop Lab, which will be available for use in early 2019.

• Slack: We have collaborated with the Fred Hutch Bioinformatics Interest Group (FHBig) which will be hosting our “Coop Communities” to continue to foster discussion and peer-to-peer support via their Slack team. Use this link to sign up, and check out this blog post for a quick-start guide to this online discussion community.

• Coop administration: We are thrilled to have Anders McConachie join the Coop team as our administrator. Anders has been with the Hutch Data Commonwealth group for over two years. Anders will help with calendar upkeep, newsletter distribution, scheduling, and event coordination. Welcome Anders!  

• Wondering what’s next for The Coop? Check out our public Trello board

News Items & Events

• Fred Hutch Wiki Writer-Editor Program openings: The new Wiki Writer-Editor program is expanding.  Applications for the Biomedical Data Science Wiki Writer-Editor program are now being accepted on a rolling basis. If you are a current Fred Hutch based postdoc, staff scientist or research specialist in any Division, we welcome you to send in a brief application to write and edit content for the Fred Hutch Wiki site: sciwiki.fredhutch.org. A monthly stipend is provided for a 3 month term with approximately ~3 hours per week appointment. Email apaguiri at fredhutch.org for more information or see instructions for applying at our CenterNet site here:  https://centernet.fredhutch.org/cn/u/bdsc/sciwiki.html (internal to Hutch)

• FHBig Monthly Meeting: FHBig will have a journal club style meeting on January 10th at 1:00pm-2:00pm in Arnold M3-A805, discussing analysis methods for DNAseq. If you would like to post a flyer on announcement boards in your building, email jlsmith3 at fredhutch.org. The following monthly meeting in February will have Jason Underwood from Pacific Biosciences (PacBio) providing a short talk with time for Q&A about long-read SMRT-seq technology.  

• R-Ladies Seattle is holding a meetup at Fred Hutch on Wed, Jan 23 at 6PM on Data Structures in R: Theory and Applications. There will be two speakers: Robin Reynolds-Haertle, technical writer at Google; and Hutch’s very own Chao-Jen Wong, bioinformatician in Tapscott Lab at Fred Hutch. More info on meetup.com

• NCBI Hackathon: The Coop is hosting an inclusive, community-focused NCBI-style hackathon (aka "The FHackathon") February 4-6, that will focus on building pipelines and data science tools broadly applicable to at least a part of the data science community. Please see this document for more information and to register to participate! The deadline is Friday, January 11.

Upcoming Trainings

• Software Carpentry Bootcamp Jan 22-25 (1-4 pm each day). This workshop is currently full, but feel free to add yourself to the waitlist in Hutch Learning to help us plan future trainings! This workshop will cover task automation with Unix (bash) shell scripting, version control with Git (on command line), and programming with Python: data structures, loops, conditionals, creating functions, errors and exceptions, defensive programming. Read more about Software Carpentry at https://software-carpentry.org/about/. Contact Kate Hertweck for more information.

• Current fredhutch.io course offerings include Intro to R, Intro to Python, and Intro to Git and GitHub. Watch Hutch Learning for scheduling of these and additional courses under development starting in 2019.

• Kate will be hosting office hours for fredhutch.io on Tuesdays from 9am to noon in M1-B153 (Arnold). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!

Nov 2018 Coop News

Hello Coop Community! This is the first official Coop Newsletter, which we will distribute about once a month via the listserv. The newsletter will follow the basic template below.

For this first communication, we wanted to clarify the purpose of The Coop. It is first and foremost a cooperative - that is, it’s a group of individuals working towards common goals. These individuals include you, your lab mates, existing groups, and future people interested in engaging in any way bioinformatics and data science at the Hutch. Goals for The Coop are better communication, better coordination for data science events that are relevant and timely, and support for internal and external collaborations at Fred Hutch around bioinformatics and data science. What The Coop does next is up to you! Read more on the Coop CenterNet Page.

First Community Meeting

Attend the 1st community meeting on Friday Dec 7 at 11 am! Event in CenterNet. Topics:

• Rachel Galbraith will be reviewing the results of the recent Hutch-wide bioinformatics survey
• Discuss communication for The Coop (listservs, Slack, CenterNet etc.)
• Discuss future plans for The Coop community meetings. We plan to have community meetings once a month with rotating topics.

Upcoming Events and Seminars

• FHBig will be celebrating their one-year anniversary and progress on the Biomedical Data Science Wiki on Dec 6 (full agenda and CenterNet event)

• In partnership with Philanthropy and the Hutch Data Commonwealth, the Hackathon powered by AWS is scheduled for Dec 7-8 (CenterNet event)

• The Coop is hosting an inclusive, community-focused NCBI-style hackathon (aka "The FHackathon") February 4-6, that will focus on building pipelines and data science tools broadly applicable to at least a part of the data science community.  There is still time to submit your ideas for hackathon projects, and keep an eye on the Biohackathon page to register to participate in coding for the in-person event!

• Data Science Affinity Group (DSAG) and Coop seminars are combining efforts. The first seminar will be in January; keep an eye out on The Coop CenterNet page for this and other events.

News Items

• Work is underway to convert M1-B406 (Arnold) into a classroom, co-working, and small group meeting space for computational work called Coop Lab, which will be available for use in early 2019.

• The Coop Launch was a success! See the transcribed brainstorm boards and photos.

• Wondering what’s next for The Coop? Check out our public Trello board

• We need help filling out the list of bioinformatics and data science groups at Fred Hutch. Each group needs a short description and contact person. If you can help, please send a note to coophelp at fredhutch.org

• We have collaborated with the Fred Hutch Bioinformatics Interest Group (FHBig) which will be hosting our “Coop Communities” to continue to foster discussion and peer-to-peer support via their Slack team. Use this link to sign up, and check out this blog post for a quick-start guide to this online discussion community.

• The Fred Hutch Biomedical Data Science Wiki project has openings for more Wiki Writer-Editors (with stipend!)!  See the Wiki here, more about the Wiki Writer-Editor Program here or email Amy Paguirigan for more information or to apply.  This project is creating a data oriented documentation resource for Fred Hutch investigators curated by current staff working in a range of disciplines from clinical research to IT professionals.  Come contribute your piece of the puzzle!!

Upcoming Trainings

• Current fredhutch.io course offerings include Intro to R, Intro to Python, and Intro to Git and GitHub. Watch Hutch Learning for scheduling of these and additional courses under development starting in 2019.

• Kate will be hosting office hours for fredhutch.io on Tuesdays from 9am to noon in M1-B153 (Arnold). Feel free to stop by and ask about bioinformatics and data science resources and training at the Hutch!