PROGRAMMER/ANALYST II G. OPPENHEIMER CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE UNIVERSITY OF CALIFORNIA, LOS ANGELES
Background: The G. Oppenheimer Center for Neurobiology of Stress and Resilience (Mayer Lab) in the Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at the University of California, Los Angeles is seeking a full time Programmer/Analyst for a multi-site funded translational research group studying brain-gut microbiome interactions in obesity and functional pain disorders including irritable bowel syndrome (IBS), chronic pelvic pain and interstitial cystitis, and vulvodynia.
This position will use multimodal MRI sequences to study structural and functional circuit dynamics cross sectionally and longitudinally within a dimensional systems biology approach. The programmer’s main responsibilities include: programming and optimizing automated data quality control, preprocessing, computational, and analyses pipelines for large scale multimodal brain imaging and biological data. The candidate should have a strong programming background in one or more of the following areas: bioengineering engineering, computer science, statistics, physics, and/or neuroscience. There will be opportunities to address basic and pathophysiological systems questions, in addition to work in an environment that emphasizes translational and clinical research skills (e.g. target discovery, individualized treatment development and biomarker/predictor development).
The G. Oppenheimer Center of Neurobiology of Stress and resilience is a dynamic multidisciplinary group directed by Emeran A. Mayer, MD, PhD conducting clinical, translational and basic neuroscience research. You will work directly with him and an array of principle investigators, collaborators and co-investigators.
Duties and Responsibilities: The Scientific Programmer and Data Analyst responsibilities will include, but are not limited to: 1. Maintain and continue to develop a full-stack application for managing and analyzing neuroimaging data <>. The back-end consists of ~9000 lines of Matlab code for processing data and over 10000 lines of MySQL stored procedures and standard SQL for triggers, views, etc. The front-end consists of ~10000 lines of Javascript/JQuery and PHP code that allows for data entry and reporting. This application is in production and stable. 2. Programming and optimizing automated data quality control, preprocessing, computational and analyses pipelines for large-scale multimodal brain imaging, including resting‐state and task-based fMRI, DTI and volumetric data. 3. Implement and support statistical analyses and scripts for biological (e.g. microbiome, genetic, etc.), behavioral, clinical and neuroscience data. This will include performing mathematical calculations/statistical analyses needed for scientific research 4. Implementation of iCloud processing and analyses pipelines such as the Human Connectome Project. 5. Implementation of data visualization programs on MRI and biological data 6. Process and analyze fMRI data: 1st level analysis 7. Work closely with data management specialist on data requests and system upgrades This would include assisting in the creation of databases, query tools for data mining, and documentation on their effective use. 8. Create and update ‘standard operating protocol’ (SOP) documents for various CNSR lab studies and/or procedures 9. Coordinate data integration from multiple ongoing studies 10. Train students and create learning tutorials for basic quality control and preprocessing of neuroimaging data. 11. Maintain detailed logs of work flow, generated codes and scripts, and documentation of processes 12. Communicate issues and concerns as they arise to PIs, nurses and other relevant research staff
Required Qualifications: B.A., B.S. Masters or equivalent with background in bioengineering engineering, computer science, statistics, physics, and/or neuroscience. Quantitative and extremely proficient with multiple neuroimaging analysis platforms (HCP Pipeline, FreeSurfer, SPM, FSL, AFNI, GIFT, TrackVis, CONN, etc.). Strong programming skills and comfort with diverse computing environments required (Matlab, UNIX/BASH language, MySQL, PHP, Javascript/JQuery are essential). Strong background in statistics and statistical software scripting (e.g. R, Python, QIIME). Experience with data visualization (d3.js or other is a plus) Strong interpersonal skills and a high level of organization with careful attention to detail are absolutely required. This position requires a high degree of motivation, organization, and self‐sufficiency, although some training and supervision will be provided.
Additional Qualifications: Experience with neuroimaging, biological, and behavioral databases is an advantage. Experience with network analyses, machine learning and modeling confer a significant advantage. Graphic or Web design skills are considered a plus, but not required for consideration.
Additional Information: Applications must be sent by email to Dr. Arpana Gupta (AGupta@mednet.ucla.edu mailto:AGupta@mednet.ucla.edu) CCing Melenie Rosales (MRosales@mednet.ucla.edu mailto:MRosales@mednet.ucla.edu) and Cathy Liu (clliu@ucla.edu mailto:clliu@ucla.edu) Please include a CV, cover letter and names of three references.
Arpana Gupta, Ph.D. Arpana Gupta, Ph.D. Assistant Professor Director, Neuroimaging Operations Core G. Oppenheimer Center for Neurobiology of Stress and Resilience Ingestive Behavior and Obesity Program Vatche and Tamar Manoukin Division of Digestive Diseases David Geffen School of Medicine UCLA CHS 42-210 10833 Le Conte Avenue Los Angeles, CA 90095-7378 http://uclacns.org/
Email: aagupta9@gmail.com OR AGupta@mednet.ucla.edu
