BroadE workshops bring researchers in the extended Broad community together so they can learn from one another. BroadE workshops (the 'E' stands for education) offer insights and share hands-on training in breakthrough technologies, high-throughput methods, and computational tools not typically found in conventional research labs. Through this ongoing series, which is open to Broad staff and to researchers at MIT, Harvard and Harvard-affiliated hospitals, the Broad community hopes to extend the impact of its science and openly share new methods.
New Registration System
It’s official — BroadE is a rousing success! In fact, demand is so high that our workshops quickly reach capacity, sometimes only minutes after being posted.
To meet this overwhelming demand and promote access to all in our community, we will repeat our most popular workshops during the coming year.
In addition, we will implement a new registration system for BroadE workshops occurring in June 2013 and later. Going forward, when a BroadE workshop is announced, we will also open a one-week application period. Participants will be selected from the pool of applicants who register during this period. In selecting participants from this pool, we will consider:
- the applicant’s home institution
- the applicant’s lab
- whether the applicant has participated in previous workshops
This new registration practice will help us to ensure that BroadE workshops reach a diverse, balanced group of Broadies.
Best Practices For Variant Calling With The GATK
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.
June 21 at 5:00 p.m.
The workshop will last two days, divided into lecture-style sessions in the morning and optional hands-on sessions in the afternoon (note that for practical reasons, attendance at the latter will be limited, so be sure to sign up early). In the morning, you’ll hear from the GATK development team and invited guests, who will explain the rationale, theory and real-life applications of the Best Practices. In the afternoon, the GATK team will help you work through interactive exercises and tutorials in which you will apply the Best Practices to real datasets.
All participants should be familiar with general next-gen sequencing terms and data formats. The lecture-based morning sessions are open to all existing, new or prospective users of the GATK. The hands-on afternoon sessions are restricted to existing users of the GATK who are familiar with the command-line work environment and at least capable of running simple analyses as described in an online tutorial.
Using CellProfiler for Biological Image Analysis
This workshop will instruct participants in the use of CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis. Attendees are encouraged to contribute sample images from their assays as part of the demonstration. We will also briefly discuss the basic principles of supervised machine learning in order to score phenotypes where phenotypic differences between samples are not visible by eye.
July 22 at 9:00 a.m.
July 26 at 5:00 p.m.