Training and Finding Help

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

At FredHutch

Courses

fredhutch.io offers frequent, on campus courses on a topics such as R, python or GitHub, and information about previous and upcoming courses is on their site. In order to sign up for courses, go to MyHutch and click on Hutch Learning to see currently available courses and register for them. fredhutch.io also helps coordinate additional events and specialized classes in collaboration with The Coop (see below).

Community Groups

The Coop (link requires login) 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. 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.

The Coop and FHBig also support community groups that meet regularly to discuss topics in 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.

• Data visualization group: Develops visualizations from data released by TidyTuesday; see #data-viz on The Coop Communities Slack

• Python coding group: TBA, see #python-user-comm on The Coop Communities Slack

• R coding group: Discusses R packages and troubleshoots code of participants; see #r-user-comm on The Coop Communities Slack

• Software design group: Discusses issues in software engineering and interface design, invites speakers on specific topics and participants share their coding projects; see #software-engineers on The Coop Communities Slack

Office Hours

Several groups on campus host weekly or monthly office hours to provide assistance on computational 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. 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 Information Security Office (ISO) and Hutch Data Commonwealth (HDC) Compliance Office 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.

• 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.

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.

Online Learning

• 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