Current Positions

Job Summary
This position will provide systems administration support as applied to research in AI, bioinformatics, genetics, genomics, imaging, proteomics, and structural biology in a highly interdisciplinary, dynamic and team-based environment. The Systems Administrator will consult with users on  hardware and software solutions, define systems scope, and provide recommendations for all systems supported infrastructure as part of regular operations, focused on high-performance computing (HPC). This position also provides systems infrastructure provisioning, configuration, and support in a timely, efficient manner. They will work a fixed schedule but require flexibility as some work must be performed outside of regular business operating hours. The Systems Administrator may also be required to act in an on-call capacity in the event of major service disruptions.

Organizational Status
The position operates in the context of the Michael Smith Laboratories at the Point Grey Campus. The position’s focus is on satisfying the needs of faculty members with advanced compute requirements in design, administration and support of high-performance computing systems. They will work in close partnership with the IT Director, UBC Advanced Research Computing, and other UBC IT staff. The position will report directly to the IT Director with oversight from the Data Science IT advisory committee.

Work Performed

For the purposes of this position, HPC includes database servers, parallel computing clusters, compute servers, distributed and cloud computing, web applications and associated software, network and hardware infrastructure used for research. Other IT domains such as email and desktop support are addressed by other personnel.

• Deploys new hardware, software, or security updates, and provide issue resolution related to hardware or software used in HPC systems

• Implements new technologies and service as well as supporting existing technology and services
• Implements, manages and maintains industry standard infrastructure and services, largely centered on self-provisioning and automation
• Ensures appropriate security is maintained across all technologies and service
• Writes and maintains documentation in accordance with prescribed standards
• Trains and assists laboratory members on the use of the systems
• Configures, installs and maintains server and storage infrastructure, virtualization infrastructure, backup and disaster recovery infrastructure, patch management
• Performs assessments, diagnostics and issue resolution
• Formulates and defines system scope and objectives and recommends a strategy, potential solution, or “work-around”
• Compiles costing statistics for evaluation, makes recommendations on purchase of hardware software and network equipment
• Monitors and analyzes systems issues and provides recommendations for all systems supported infrastructure as part of regular operations
• Designs, provisions, and configures systems
• Acts as a liaison between technical groups and stakeholders to coordinate the system installations and ensures technical compatibility and satisfaction
• Designs solutions to resolve system-related problems, meet user requirements, and streamline system work flows
• Provides recommendations for improving procedures and coordinating system implementation
• Integrates development of best practices, standards, procedures and quality objectives across systems infrastructure or platforms
• Maintains appropriate professional designations and up-to-date knowledge of current information technology techniques and tools
• Performs other related duties as required

Supervision Received

The position will work independently but receives direct supervision from the IT Director Michael Smith Laboratories. They will work closely with other MSL and university IT staff. Work is reviewed in terms of achievement of specific task objectives.

Supervision Given

None

Consequence of Error/Judgement

Decisions and actions will have a direct impact on how efficiently and effectively applications will perform and function. Errors could result in serious damage to computing and networking equipment, loss of research time, computing and networking services, and/or loss of all data communications, as well as financial loss to the departmental and/or researcher grants. Failure to act decisively could have a detrimental effect resulting in data loss or exposure of personal information and could significantly impact the educational and research mission of the department and damage UBC s reputation.

Work will involve sensitive data and it is expected to follow all UBC Information Security Standards, and to exercise judgment, diplomacy, and tact in all interactions.

Minimum Qualifications

Undergraduate degree in a relevant discipline. Minimum of three years of related experience, or the equivalent combination of education and experience.

• Willingness to respect diverse perspectives, including perspectives in conflict with one’s own
• Demonstrates a commitment to enhancing one’s own awareness, knowledge, and skills related to equity, diversity, and inclusion

Preferred Qualifications

University degree in Computer Systems Technology, Computer Science, Mathematics, Statistics, Physics, or a similar discipline. Experience working in an academic research setting an asset.

Skills

The System Administrator demonstrates strong technical, analytical and problem-solving skills in order to design, install, trouble-shoot and maintain computational infrastructure. Experience supporting Linux server configurations is necessary. Must be able to move and lift a wide assortment of equipment. Expected to have the skills to plan and carry out multiple tasks and projects, to prioritize and organize effectively, to work under pressure, and to meet established timelines. Ability to work independently and in a team environment. Appropriate professional certifications are an asset. Demonstrated willingness to learn and continually upgrade skills is essential. As this position also involves extensive personal interaction as well as via phone and email, excellent written and verbal English communication skills are critical.

The following is a more extensive list of skills that are desirable at time of hire, or must demonstrate an ability to acquire:

• Advanced Linux shell programming
• Source-code management with Git
• Database administration/SQL
• MySQL database clustering/replication
• Systems programming in Python and Perl
• Administration of R and RStudio
• Server & Configuration Management & Automation using Salt Stack in both an Ubuntu and Red Hat distribution Linux environment
• Networking knowledge with the base understanding of TCP/IP, DNS, DHCP, and similar software/protocol stacks
• Web application configuration experience with PHP, Tomcat, and Apache
• Identity Management experience using 389 Directory and OpenLDAP
• NFS, CIFS, and iSCSI
• Juniper, Dell, and HP Switch Programming
• Linux filesystems such as XFS, EXT2/3/4, and ZFS
• Familiarity with Physical Server Hardware e.g. Dell, HP, Supermicro, and Sun Microsystem Servers
• Server Rack, PDU, and UPS Backup Power Management
• Self-provisioning and automation using PXE, Kickstart, Cobbler, FOG, Foreman, and similar toolkits
• Commercial cloud computing environments (e.g. Google, Amazon, and Azure)
• Continuous integration systems such as Bamboo, Jenkins, and OpenShift
• Parallelization using job schedulers (OpenMPI) for HPC using software such as Rocks, OpenMPI, Torque, Maui, and other job schedulers
• Systems security practices such as SELINUX enforcement, hardening of servers, and securing of web applications

Application link: https://ubc.wd10.myworkdayjobs.com/en-US/ubcstaffjobs/job/Systems-Administrator_JR19524

Posting End Date

January 7, 2025

Note: Applications will be accepted until 11:59 PM on the day prior to the Posting End Date.

Postdoctoral Fellow in Cancer Epigenetics and Genomics Using Novel Sequencing Technologies

The Michael Smith Laboratories at the University of British Columbia in Vancouver, Canada, invites applications for a Postdoctoral Fellow (PDF) to join the Multi-omic Analysis of Treatment Resistance and Cancer Heterogeneity (MATCH) lab under the supervision of Dr. Marco Marra. The successful candidate will work on a project that uses novel sequencing technologies such as long-read sequencing and single-cell sequencing to study cancer datasets. They will join a dynamic team of researchers working towards the central goal of using next-generation genomics to improve lives of Canadians living with cancer.

The Technology

This project will involve the use of several novel sequencing technologies, specifically, long-read sequencing, short-read sequencing, and single-cell sequencing. Long-read sequencing generates sequencing reads averaging tens of thousands base pairs, enabling better mapping and resolution of complex structural variations and repetitive regions, with the added benefit of including all base modifications including DNA methylation. Single-cell sequencing uncovers cellular heterogeneity by profiling the individual cells, revealing insights into cancer heterogeneity and cell populations. Short-read sequencing provides accurate, high throughput data, ideal for identifying single nucleotide variants, expression profiling, and performing bulk analyses. Together, these technologies can be used to better resolve the complexities of cancer genomes: long-read sequencing informs large structural changes and epigenetic information, short-read sequencing ensures depth and variant accuracy, and single-cell sequencing deciphers cell-specific interactions, collectively transforming our understanding of the disease.

The Opportunity

The PDF will leverage novel sequencing technologies and bioinformatics analysis to explore the genomic and epigenomic alterations found in cancer, specifically virus-driven cancers. This will require integration of data from whole-genome, transcriptome, and methylome analyses to investigate the epigenetic impact of large genomic changes on cancer genomes. The candidate may develop and implement bioinformatics tools and workflows to process and analyze multi-omics datasets, enabling insights into complex genomic changes. They will facilitate projects in collaboration with local and international scientists, clinicians, and public health researchers to make meaningful impacts to cancer detection, diagnosis, and treatment.

Qualifications and Experience

• PhD in Bioinformatics, Computational Biology, Statistics, Genetics/Genomics, or a related discipline
• Proficiency with at least one of the following: long-read sequencing, short-read sequencing, and single-cell sequencing, including data generation and analysis
• Strong publication record in high-impact peer-reviewed journals
• Excellent written and verbal communication skills with experience presenting findings at scientific conferences
• Proficiency in bioinformatics programming languages, such as Python, R, and Bash
• Extensive experience in multi-omics analysis, including whole-genome, transcriptome, and methylome sequencing
• Strong skills in developing, implementing, and optimizing bioinformatics workflows and tools
• Experience with high-performance computing environments and version control systems like Git
• Proven success working in multidisciplinary teams, contributing to collaborative research projects
• Familiarity with cancer genomics or viral genomics research is an asset.

The expected pay for this position is $55,000 to $60,000 per year. Salary is competitive, negotiable, commensurate with education and experience.

Application Process

Interested applicants should submit a cover letter, a curriculum vitae including a list of publications, and contact details for 3 references to the UBC Careers portal at https://ubc.wd10.myworkdayjobs.com/en-US/ubcfacultyjobs/job/Postdoctoral-Research-Fellow_JR19540-1. Applications should be submitted no later than the posting end date.

The appointment will be for one year commencing March 1, 2025 with a possibility for extension, subject to satisfactory performance and funding.

Posting End Date

February 6, 2025

Note: Applications will be accepted until 11:59 PM on the Posting End Date.

Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged. We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.

Dr. Sabrina Leslie at UBC Michael Smith Laboratories is recruiting a graduate student with interest in biophysics and nanomedicines. Our group develops and utilizes single-molecule fluorescence microscopy techniques to study lipid nanoparticle loading and delivery of biomolecules in cell-like environments. We’ve developed the Convex Lens-induced Confinement (CLiC) imaging platform, which makes it possible to watch individual, freely diffusing biomolecules/ nanoparticles as they search for and bind to each other, allowing us to make measurements that are not possible with other methods. This technique is applied both to basic biophysical research and development of drugs and therapeutics.

Project: Nanoparticle analytics

This project will study the structure and structural transitions of nanoparticles in controlled environments, to help develop nanoparticle-based drug delivery platforms. Nanoparticles are an emerging technology used to encapsulate drugs for delivery into the body. Upon an environmental shift, the structure of the nanoparticle changes, releasing the drug. The goal of this research will be to characterize these dynamics and understand drug delivery mechanisms.

Training: Graduate students in the Leslie Lab receive training in single-molecule microscopy, specializing in the CLiC imaging technique pioneered in our lab; bulk characterization techniques such as Dynamic Light Scattering, fluorimetry, and gel electrophoresis; and computational modelling and analysis. The candidates will work with sophisticated DNA/RNA constructs as well as complex lipid nanoparticle formulations, with exposure to molecular design of oligotherapeutic compounds and biomimetic delivery vehicles. The training environment will include interactions with a start-up company, ScopeSys Inc., which is commercializing CLiC technology; as well as collaborators in pharmaceutical science, biochemistry and medicine.

We are looking for a well-organized, enthusiastic team player who enjoys lab work and troubleshooting scientific instrumentation. Background/training in biochemistry, quantitative biology, pharmaceutical sciences or surface chemistry is an asset. Proficiency with a musical instrument and/or dungeons and dragons are also assets. The successful candidates must have a passion for innovation and pushing scientific and engineering capabilities to the forefront of what is possible today.

Application deadline: April 30, 2025. Applications will be considered on a rolling basis.

To apply, please send a cover letter and CV to leslielab [at] msl.ubc.ca.

Dr. Sabrina Leslie at UBC Michael Smith Laboratories is recruiting a graduate student with interest in biophysics, nanoscience, biotechnology, engineering and computational analysis. Our group develops and utilizes single-molecule fluorescence microscopy techniques to study interactions of biomolecules in cell-like environments. We’ve developed the Convex Lens-induced Confinement (CLiC) imaging platform, which makes it possible to watch individual, naturally fluctuating biomolecules as they search for and bind to each other, allowing us to make measurements that are not possible with other methods. This technique is applied both to basic biophysical research and development of drugs and therapeutics.

Project: Oligonucleotide therapeutics

Antisense oligonucleotides (ASOs) are an emerging treatment for genetic diseases. They are snippets of modified DNA designed to bind to mRNA produced by a detrimental gene and targeting it for destruction. The goal of this research project will be to characterize ASO-mRNA binding dynamics to improve drug and treatment development.

Training: Graduate students in the Leslie Lab receive training in single-molecule microscopy specializing in the CLiC imaging technique pioneered in our lab, bulk characterization techniques such as Dynamic Light Scattering, fluorimetry, spectrophotometry, and gel electrophoresis, and computational modelling and analysis. The candidates will work with sophisticated DNA/RNA constructs as well as complex lipid nanoparticle formulations, with exposure to molecular design of oligotherapeutic compounds and biomimetic delivery vehicles. The training environment will include interactions with a start-up company, ScopeSys Inc., which is commercializing CLiC technology; as well as collaborators in pharmaceutical science, biochemistry and medicine.

Interested candidate should have a degree in physics, engineering, or biophysics, with passion for lab work and troubleshooting scientific instrumentation, and is creative, versatile and well-organized. Strong interest in optics and instrumentation is an asset. Proficiency with a musical instrument and/or dungeons and dragons are also assets. The successful candidates must have a passion for innovation and pushing scientific and engineering capabilities to the forefront of what is possible today.

Application deadline: April 30, 2025. Applications will be considered on a rolling basis.

To apply, please send a cover letter and CV to leslielab [at] msl.ubc.ca

Dr. Sabrina Leslie at UBC Michael Smith Laboratories is recruiting a graduate student with interest in biophysics, nanoscience and biology. Our group develops and utilizes single-molecule fluorescence microscopy techniques to study interactions of biomolecules in cell-like environments. We’ve developed the Convex Lens-induced Confinement (CLiC) imaging platform, which makes it possible to watch individual, naturally fluctuating biomolecules as they search for and bind to each other, allowing us to make measurements that are not possible with other methods. This technique is applied both to basic biophysical research and development of drugs and therapeutics.

Project: Effects of topology on DNA structure and interactions

DNA supercoiling drives structural transitions within a DNA molecule. This project will study the dynamics of such transitions, how multiple transitions within the same molecule can compete with one another, and how such transitions affect protein-DNA interactions. The goal of the research project will be to better understand the role of these structural transitions in gene regulation and bridge the gap between in vitro and live cell studies.

Training: Graduate students in the Leslie Lab receive training in single-molecule microscopy, specializing in the CLiC imaging technique pioneered in our lab; bulk characterization techniques such as Dynamic Light Scattering, and fluorimetry; standard molecular biology techniques including cell transformation, and gel electrophoresis; and computational modelling, image processing and analysis. The training environment will include interactions with a start-up company, ScopeSys Inc., which is commercializing CLiC technology; as well as collaborators in pharmaceutical science, biochemistry and medicine.

We are looking for a well-organized, enthusiastic team player who enjoys lab work and troubleshooting scientific instrumentation. A successful candidate would have experience with or interest in DNA structure and function, fluorescence microscopy, statistical mechanics, mathematical modelling, and computer programming. Background in biophysics, molecular genetics, quantitative biology, or a related field is an asset. Proficiency with a musical instrument and/or dungeons and dragons are also assets. The successful candidates must have a passion for innovation and pushing scientific and engineering capabilities to the forefront of what is possible today.

Application deadline: April 30, 2025. Applications will be considered on a rolling basis.

To apply, please send a cover letter and CV to leslielab [at] msl.ubc.ca.