Training, Community and Finding Help

There are a variety of resources for training on various aspects of bioinformatics, analytics and data skills available at the Fred Hutch, in the Seattle area and on the web.

Resources At Fred Hutch

In Person Courses

fredhutch.io offers frequent, on campus courses on a topics such as R, Python and GitHub; course descriptions can be found here. Fred Hutch and SCCA employees can register for these courses by going to MyHutch and clicking on Hutch Learning. Search for “fredhutch.io” to view and register for all currently available courses. fredhutch.io also helps coordinate additional events and specialized classes in collaboration with The Coop (see below).

Community Groups

The Coop is the Fred Hutch Bioinformatics and Data Science Cooperative, and works to share information and resources about computational work across the Hutch. The Coop maintains a listserv, calendars of data science events, and The Coop Communities Slack, supported by FHBig. FHBig is the Fred Hutch Bioinformatics Interest Group, a community-based group that hosts a blog and facilitates information sharing among the bioinformatics research community at the Hutch. Hutch employees can learn more through the links above or by emailing coophelp wiht questions or to be added to our email/newsletter list.

The Coop and FHBig also support community groups that meet regularly to discuss topics ranging from basic data literacy skill building to reproducible computational methods. To learn more about what to expect from these meetings, please visit our Community Groups GitHub repository. Current meeting schedules and locations are available on the Google calendar, and please contact the Coop (coophelp at fredhutch.org) or the relevant channel in The Coop Communities Slack with any questions.

• Coop Monthly Meetings: The Coop hosts monthly meetings that rotate among a few different formats, including:
  • Community meetings: Reports and updates from different groups across campus. Join us to learn about projects and events happening in our community!
  • Panel discussions: Hutch and visitors to campus discuss topics relevant to data-intensive research.
  • Seminars: Topics include tools, approaches, and concepts related to data-intensive research.

• Data Visualization Group: Develops visualizations from data released by TidyTuesday. All programming languages (and even non-coders!) are welcome. Notes about this group can be found here. See the #data-viz channel on The Coop Communities Slack for more information.

• Nextflow User Group: Discusses issues related to the use of Nextflow (and other workflow managers like Cromwell) at Fred Hutch. The group welcomes Nextflow users of all levels of expertise as well as those just learning about the tool. See the #nextflow channel on The Coop Communities Slack for more information.

• Python User Group: The Python User Group meets weekly to discuss programming, data analysis, and troubleshooting in python as well as dedicate one meeting a month to general software development; topics will be announced ahead of time. Bring your lunch, code, questions, and thoughts! Python coders of all levels of expertise are welcome. Notes about this group are recorded here, and check out the #python-user-comm channel on the Coop Communities Slack for announcements.

• R User Group: The R User Group meets weekly to discuss programming, data analysis, and troubleshooting in R. Bring your lunch, code, questions, and thoughts! R coders of all levels of expertise are welcome. Notes about this group are located here, and check out the #r-user-comm channel on the Coop Communities Slack for announcements. Note: If you do not have a laptop available to you we still want you to come!! You can email code privately ahead of each event to Amy Paguirigan (apaguiri at fredhutch.org).

• Technology Exchange: Informal learning forum for employees in technology-focused jobs to share technical skills. This group is most appropriate for individuals who want to discuss the technical details of tools commonly used in positions focused on administration and infrastructure. However, anyone is welcome to attend this forum, and many topics will be relevant to researchers in positions that require technical skills. Subscribe to the TechExchange mailing list for more information.

• Retired Community Groups: All of our groups were created because of the needs voiced by our community. Sometimes those needs change, and we’re happy to respond by refocusing our efforts. The following groups have been retired, but are noted here for reference purposes:
  • Software design group: Discusses issues related to software engineering and interface design and invites speakers on specific topics and participants to share their coding projects. This group is not focused on a specific programming language, but rather on issues common across software projects. Notes from this group can be found here. Discussions about this topic are now included periodically in the Python User Group
  • Shiny User Group: The Shiny User Group meets once monthly to discuss this method of using R to create interactive web applications for visualizing data analysis. Notes about this group are located here. Discussions about this topic are now included periodically in the R User Group

Office Hours

Several groups on campus host weekly or monthly office hours to provide assistance on data related tasks. Please visit Centernet or the Google calendar for current scheduling, locations, and contact information.

• Bioinformatics (Shared Resources) offers consultation on a variety of issues related to experimental design and bioinformatic analysis. They are able to answer questions on topics including: experimental design, exploring data visually (e.g., IGV, Loupe Cell Browser), generating figures for manuscripts, and developing customized workflows for unique problems. These office hours are not currently being held on a regular basis; see the Shared Resources website for more information, and email bioinformatics to make sure there is time/space available during their scheduled events.

• Data Ethics/Compliance/Security: Staff from the Hutch Data Commonwealth (HDC) Compliance Office with expertise in information security are available to answer questions related to secure data management and resources at the Hutch for security compliance.

• The Coop: Staff are available to assist researchers in getting started with coding and orienting staff to resources for improving their coding, including troubleshooting application of code to research questions.

• REDcap: REDCap is a secure web application for building and managing online surveys and databases and is managed by Collaborative Data Services (CDS) at Fred Hutch. Staff are available to answer questions related to REDCap functionality and troubleshooting. You can also discuss REDCap issues with staff and other researchers on the #redcap-user-comm channel on The Coop Communities Slack.

• SciComp General Consulting: Scientific Computing (SciComp) is the group in Hutch Data Commonwealth (HDC) that manages basic account access for research computing resources, including data storage and shared computational cluster use. Staff are available to answer questions related to access and usage of Hutch resources for computational research.

• SciComp Next Gen/HPC Office Hours: In addition to general consulting (see above), Scientific Computing (SciComp) supports researchers interested in emerging technologies like next generation sequencing and cloud computing. Staff are available to answer questions about getting started building analytical pipelines in the cloud, and generally making computation more scalable and reproducible.

Resources In Seattle

• UW Biostatistics Summer Institutes offer yearly intensive courses over the summers on a wide variety of topics.
• Meetup hosts various coding groups that meet regularly to share skills and provide networking opportunities. RLadies Seattle and Seattle UseR both include leaders from Fred Hutch.

Resources on the Web

The following sites include content that one or more community member has found useful. Most of them include at least some free content, while others require a paid subscription.

• Biostar Handbook: A Beginner’s Guide to Bioinformatics
• CalTech Learning from Data
• The Carpentries, with lessons from Data Carpentry and Software Carpentry
• Cognitive Class: Data science and cognitive computing courses
• Coursera, including courses on Data Science and Bioinformatics
• CodeAcademy
• DataCamp
• DataQuest
• edX, including courses in Data Analysis and Statistics and Bioinformatics
• The Open Source Data Science Masters
• ROSALIND interactive bioinformatics problem set
• Udacity has courses on Data Science
• Udemy has a section on Data Science