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.

• Coop community meetings: The Coop hosts community meetings once a quarter to share information from the data science community at the Hutch. Join us to learn about projects and events happening in our community!

• Data visualization group: Develops visualizations from data released by TidyTuesday. All programming languages (and even non-coders!) are welcome. See the #data-viz channel on The Coop Communities Slack for more information.

• Nextflow 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 coding group: Discusses methods of programming in Python and troubleshoots code of participants. Python coders of all levels of expertise are welcome. See the #python-user-comm channel on The Coop Communities Slack for more information.

• R coding group: Discusses R packages, R code and troubleshoots code of participants. R coders of all levels of expertise are welcome. See the #r-user-comm channel on The Coop Communities Slack for more information.

• 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. See the #software-engineers channel on The Coop Communities Slack for more information.

• 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.

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.

• Data Science/Software Engineers: Hutch Data Commonwealth (HDC) employs teams of Data Scientists and Software Developers, who are available to answer questions related to general data management and application of common data science tools (like machine learning) to research questions.

• Fredhutch.io: fredhutch.io trains researchers in reproducible computational methods. 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 New Technologies: 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

• 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 Bioinforamtics
• 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