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We manage to release the code of every manuscript to Chen Lab GitHub Repositories.

Chen lab resource introduction

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PI Dr. Bin Chen was recruited to MSU from University of California San Francisco through the MSU Global Impact Initiative in early 2018. The Global Impact Initiative aims to recruit new researchers from the world to focus on the most challenging problems facing human civilization. Dr. Chen holds a primary appointment in the Department of Pediatrics and Human Development with a secondary appointment in the Department of Pharmacology and Toxicology in the College of Human Medicine. The resources and facilities are available through the College of Human Medicine and the University. Chen lab is located on the 7th floor in the Secchia Center medical education building, in the heart of Grand Rapids Medical Mile. Chen lab has a number of cubicles and open tables for his lab members. The office is within walking distance to the newly constructed state-of-the-art Grand Rapids Research Center (GRRC), which has space for up to 44 investigators and houses core facilities, Van Andel Research Institute , and Spectrum Health. Chen lab can access to their core facilities at internal billing rates, campus research resources as well as students. The secondary appointment in Pharmacology and Toxicology allows Dr. Chen access to graduate students through the Biomolecular Science Gateway and also the vast resources in the MSU East Lansing main campus, which is one hour away from the Grand Rapids campus. The flexible program at MSU allows Dr. Chen mentoring students from the Department of Computer Science, the Department of Computational Mathematics, Science and Engineering and the College of Osteopathic Medicine. To facilitate mentoring students and maintain collaboration with other investigators in East Lansing, Dr. Chen has one office and a few open spaces in the life science building.

Founded in 1855, MSU enrolls more than 41,000 students in 14 colleges, which offer over 165 areas of undergraduate and 76 areas of graduate specialization, making it as one of the largest universities in the United States in terms of enrollment. Dr. Chen can recruit talent from such a big pool. MSU employs approximately 3,000 faculty/staff members who are engaged in teaching, research and service. It has over 5,315 acres of land and more than 400 buildings. Research at MSU is an integral part of the academic climate and is carried on in all disciplines. There are more than 3,000 major research projects being pursued at the University. Much of the research is multidisciplinary in nature and involves cooperation and collaboration between engineers, basic scientists and clinical researchers. Cisplatin, one of the most popular anti-cancer drugs, was discovered and developed at MSU.

Dr. Chen has built up a team consisting of postdoctoral scholars, research assistants, undergraduates/graduates, medical students. The lab always welcomes highly-motivated trainees. As a computational lab, Chen lab is exploring new ways to keep high productivity. Chen lab primarily uses SLACK to communicate and manage projects. Over one hundred messages are exchanged daily by lab members. For example, its lab orientation channel shares all core resources and documents for new trainees to quickly pick up lab research; its lab technique channel serves as an internal stackoverflow to foster technical knowledge sharing and learning; its lab paper tracking channel shares the most recent interesting publications. Each project has its own channel for project discussion and one google doc for project documentation. Besides, each project has one data folder on AWS cloud and one code repository on GitHub. All key manuscripts are released in BioRxiv after submission. We believe such management would encourage open data, open code, open science and reproducible research.

Each full-time staff in Chen Lab is equipped with one Apple Mac laptop. The Lab actively works with cloud based resources provided by Amazon Web Services for sequencing analysis and deep learning research. Each big project has its dedicated instance. For example, lab members can easily process raw RNA-Seq data and make drug predictions on one instance and run deep learning modules on another. Chen Lab uses the iCER’s HPC clusters that include 596 compute nodes with more than 17,500 cores. Included in the clusters are 90 NVIDIA GPUs and 28 Xeon Phi equipped nodes. Chen Lab has purchased the buy-in cluster equipped with 128+ GB RAM for regular computational analysis.