Requisition #: 29606
Working Title: Research Bioinformatician I
Business Entity: CSMC - Cedars-Sinai Medical Center
Cost Center # - Cost Center Name: 0879063 - Heart Institute Operations
City: Los Angeles
Job Category: Research/Research Admin
Job Specialty: Research
Position Type: Regular-F/T
Shift Length: 8hr
Hours: 8am - 5pm
Days: Monday - Friday
Shift Type: Day
Weekends: As Needed
Job Posting: Summary of Essential Job Duties:
Under supervision, the Research Bioinformatician I (RBI) performs general bioinformatics analysis and software support for projects involving in omics. The RBI will manage omic data including loading and querying data from database system and public repositories, and transform and merge multilevel omic data into user-friendly formats, assist in development, test, and maintenance of modular software pipelines, provide daily bioinformatics data analysis, preliminary interpretation of the data, and reports of the results for possible publications. The RBI will also function as a systems manager for an HPC cluster installation. Tasks associated with this include working with researchers and vendors to provide and/or coordinate installation and modification of open-source and vendor-supplied software.
ESSENTIAL JOB DUTIES AND RESPONSIBILITIES:
Provides general bioinformatics analysis support for omic projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers.
Summarizes data analyses results in the form suitable as the basis for the first draft of written reports, and makes preliminary interpretations of the data.
Assists in development, testing, and maintenance of modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences.
Manages data including loading and querying data from database systems, downloading omic data from public repositories, and transforming data to the necessary formats.
Helps to identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology.
Manages day to day operations of the High-Performance Computing (HPC) cluster.
Acts as the primary HPC liaison for vendor and investigator related communication and issues.
Works with researchers and vendors to provide and/or coordinate assistance with the installation and modification of open-source and vendor-supplied software onto the HPC cluster and other servers.
Participate in HPC design and technical meetings and maintain HPC documentation as necessary.
Provide HPC support for researchers, including assistance with implementation and troubleshooting pipelines and other software used by researchers.
Conduct training classes for new HPC users
DEPARTMENT AND/OR UNIT SPECIFIC – ESSENTIAL JOB RESPONSIBILITIES:
This is a joint position between the Advanced Clinical Biosystems Research Institute (ACBRI) and the Research Informatics and Scientific Computing Core (RISCC). The primary focus will be on bioinformatics data analysis, software development and High Performance Computing (HPC) systems administration. The candidate will be working under the joint supervision of the ACBRI Bioinformatics team lead and RISCC manager.
Additional ACBRI Requirements:
• Evaluation and selection of commercial or open-source software required in assisting the proteomics database analysis, and analyzing the mass spectrometry data for its integration in pipelines
• Provides general bioinformatics analysis support and assist in development, testing and maintenance of software pipelines for mass spectrometry data, network analysis, and visualization tools and browsers.
• Coordinating with fellow programmers, scientists and technicians for providing support programming for analysis of genomic and proteomic data sequencing in various therapeutic areas and providing quality control instructions in programming
• Development of scripts to move data from one analysis module to another, typically as part of the management of large data sets (loading, transformation, report generation, quality checks, etc.).
• Aiding in software training for the scientists and technicians, maintaining the in-house tools and databases and supporting the bioinformatics team with their on-going efforts.
Education Certifications/Licensure Experience Physical Abilities Educational Requirements:
Bachelor of Science Degree in Computer Science, Electric Engineering, Computational biology, or Bioinformatics, or Master of Science preferred in relevant fields (e.g. Biology with strong quantitative training, biostatistics with concentration in bioinformatics).
Strong Background in software development and bioinformatics data analysis concepts.
Basic knowledge about the principles of gene sequencing, proteomics, transcriptomics and experience with handling bioinformatics tools including Sequence alignment, variant calling, mass spectrometry tools, Pathway analysis, Data to Knowledge tools is required
Experience in HPC architecture, engineering and implementation, including deploying, maintaining and administering a large Linux/Sun Grid Engine HPC cluster is required.
Deep knowledge of MPI and OpenMP is a plus.
Understanding of parallel computing concepts is required.
0-3 years in research environment. Background and work knowledge in algorithms, scientific computing, and machine learning or statistics, Familiar with C/C++, Java, Perl, python, and the Unix (Linux) environment, Experiences in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets, both in exploratory and pipelined fashions, will be a plus.
Any combination of academic education, professional training or work experience, which demonstrates the ability to perform the duties required for the position.
Location/Region: Los Angeles, CA (US)