Harvard Chan Bioinformatics Core Year-End Update
Happy holidays from the Harvard Chan Bioinformatics Core. We hope our annual newsletter finds you well in these challenging times. After three months at our new location at the Landmark Center in Fenway, the HBC team went remote on March 9th. We are fortunate that much of our work can be done remotely and have continued to provide consults and training while dealing with the challenges of this global pandemic. Changes to our typical routine have ranged from pivoting our training to conduct workshops on Zoom to holding group happy hours over Zoom. We feel very fortunate to be able to continue to support our research community, including working on Covid-19 related projects with Dr. Jonathan Li (BWH) and Dr. Carla Kim (BCH). Other bright spots in the year include Drs. Meeta Mistry, Rory Kirchner, Sergey Naumenko and Mary Piper welcoming new additions to their families, and the promotions of Drs. Victor Barrera and Mary Piper to Research Scientists. After eight years in the Core, Ilya Sytchev, our Senior Bioinformatics Software Developer, transitioned to a new position at the School’s Quantitative Biomedical Research Center (qBRC). We thank him for his many contributions, wish him the best in his new role, and look forward to collaborating with him in the future.
Our team of 14 provides bioinformatics consulting and training to investigators at the Harvard Chan School and across the Harvard community, with a focus on applications of high throughput sequencing (HTS). Through individual collaborations and ongoing relationships with Harvard Catalyst, the Harvard Chan-NIEHS Center for Environmental Health, the Harvard Center for AIDS Research (CFAR), the Harvard Stem Cell Institute (HSCI), Harvard Medical School (HMS), and most recently, the Dana Farber/Harvard Cancer Center (DFHCC), we supported 57 grant applications and 256 consult requests this year. We co-authored 22 publications, including papers in Cell, Nature, eLife, Science Translational Medicine, PNAS, Cancer Discovery, JCI Insight and Blood, demonstrating the wide range of science the Bioinformatics Core supports.
With funding from a Chan Zuckerberg Initiative Essential Open Source Software for Science grant and AstraZeneca, we continued to maintain and develop the core’s bcbio-nextgen platform. Bcbio-nextgen is an open source python toolkit that provides best-practice pipelines for fully automated high throughput sequence analysis. Google Scholar shows 96 acknowledgements of bcbio-nextgen software for 2020, indicating its wide usage across the globe. Some highlights from this year include improving the bcbio deployment process and its developer and user documentation, benchmarking tools for mobile element detection and copy number variation analysis leading to the integration of Scramble and PureCN, respectively, enhancing the ATAC-seq pipeline to include more comprehensive QC and standardized handling of replicates, and developing a pipeline for whole genome bisulfite sequencing analysis. Notably, the Core committed over 400 changes to the bcbio github with 12 other scientists also making contributions.
In April, the training program pivoted to online courses. We updated our workshop format and lessons to ensure that trainees were still able to get the most out of these training sessions. The in-class segment of the workshops was reduced and focused on discussions and exercises, and trainees were expected to learn content on their own between in-class segments. This transition has been very successful based on trainee feedback. We provided 16 workshops (13 online) and trained 524 researchers on basic data skills and HTS data analysis. We also provided 6 workshops (4 online) as part of our “Current Topics in Bioinformatics” series, training over 500 researchers; these popular workshops are free and open to everyone at Harvard. We continued our involvement in Harvard Catalyst courses. “Introduction to Omics Research” was offered once more this year with 561 participants, and we recorded a new online, hands-on R tutorial that will be freely available Harvard-wide in early 2021. We also continued our collaboration with Harvard’s FAS Research Computing “RC” group to make high performance computing more accessible to School researchers.
While this year has been filled with unprecedented challenges, it has also included compelling science and many opportunities to grow and learn. We thank you and our collaborators for your flexibility, commitment to science, insight and exceptional innovation. Wishing you all the best for 2021!