What are the responsibilities and job description for the Bioinformatics Cloud Engineer. position at Colorado Department of Public Health and Environment?
Department Information
Division of Disease Control and Public Health Response
This requires Colorado Residency to apply
This is Hybrid position
We are committed to increasing the diversity of our staff and providing culturally responsive programs and services. Therefore, we encourage responses from people of diverse backgrounds and abilities.
Be BOLD.....Make a REAL difference . . . and join us in serving our communities advancing Colorado's health and protecting the places we live, work, learn, and play, to create a healthy and sustainable Colorado where current and future generations thrive.
Our mission… is to advance Colorado's health and protect the places we live, work, learn, and play.
Our vision… is to create a healthy and sustainable Colorado where current and future generations thrive. In addition to free parking, access to RTD bus lines, Cherry Creek bike path and flexible working arrangements, click the link below to review additional benefits and perks!!! https://cdphe.colorado.gov/careers
Description Of Job
The Division of Disease Control and Public Health Response (DCPHR) is the department’s lead surveillance, planning and response arm for public events including communicable disease outbreaks and epidemics, pandemics, bioterrorism, and other public health and mass casualty events and disasters. The division includes the Office of Emergency Preparedness and Response; State Public Health Laboratory; Health Equity Branch, Communicable Disease Branch; Immunization Branch; Public Health Informatics, Reporting, and Refugee Branch; and Operations Branch. The Division exists to ensure that the Department has the ability to effectively prepare for, monitor, detect, diagnose, investigate, and nimbly respond to all types of conditions, events and disasters that impact the public’s health.
The Work Unit
The work unit exists to provide accurate scientific data and test results about detection, identification, and characterization of microorganisms by current molecular, genomic, and bioinformatic methods in clinical, wastewater, and environmental specimens from culture independent diagnostic tests (CIDTs), as well as following extraction of nucleic acid targets form live cultures, of bacteria, fungi, parasites, viruses, and other agents of public health concern isolated from source specimens. These data are used in timely support of patients’ diagnosis and management, epidemiological investigations of disease outbreaks, rapid response to bioterrorism events, and identification of agents affecting public health and environment.
What You Will Be Doing
The Bioinformatics Cloud Engineer within the public health laboratory oversees developing and maintaining cloud infrastructure, assisting the unit in managing and storing large genomic datasets and bioinformatic analyses, as well as in automating processes such as data storage and pipeline execution. This position is expected to apply state-of-the-art computational and cloud engineering methods and to assist in the development of innovative approaches to cloud infrastructure and software challenges that touch all aspects of NGS data. This includes but is not limited to raw data handling, pathogen identification, outbreak tracking, mapping drug-resistant determinants, development of novel NGS tests, variant analysis, genome annotation, and phylogenetics. Data and analytics involve bacterial, viral, fungal, parasitic, and human NGS data. Cloud engineering experience, coding expertise, efficient communication skills, basic knowledge of microbiology, training, and outreach are necessary requirements for this position.
Development and Maintenance of Cloud Infrastructure
This position builds and maintains cloud-based infrastructure to support large-scale genomic data analysis using Google Cloud Platform (GCP). This includes, but is not limited to, developing and operating robust, scalable, flexible, and secure cloud systems that integrate with bioinformatics analysis platforms (e.g. Seqera, Terra.Bio, AMD platform). This position adheres to and maintains security best practices and assigns appropriate user access permissions for team members and collaborators. Works closely with team members to ensure seamless orchestration of workflows and pipelines and works to automate cloud processes where feasible.
Data Storage and Management
This position oversees maintaining organized data storage and management strategies, adhering to the unit’s data retention and lifecycle policies and works to improve efficiency and cost-effectiveness of storing large scale datasets.
Pipeline Construction, Maintenance, and Execution
Perform bioinformatics data analysis on all NGS data generated in the lab. Responsible for the construction, validation, maintenance, and implementation of bioinformatics pipelines and workflows. Where applicable, move pipelines forward for CLIA validation.
Workforce Development and Consultation
As an ELC AMD Bioinformatics Resource and Training Support Site (BRR/BTL), and AMD Platform IT Security and Privacy Domain Lead (ITSP), significant time is taken to design, construct, and then implement and instruct internal, regional, and national partners. Part of this position will include providing bioinformatics and cloud engineering support to other state public health labs upon request, as well as providing training to other state public health labs through participation in the planning and presentation of instructional materials. Instruction consists of bioinformatics and genomics, but could also include topics of AMD platform implementation, cloud engineering and resource utilization, and large-scale data management and storage. Consultation of regional labs for training and resource implementation is necessary. This role will also participate in ITSP domain activities that include, but are not limited to, consultation with other public health lab partners and CDC on ITSP-related topics, bioinformatics and cloud infrastructure, and user acceptance testing.
Communication
An integral part of work within the unit is communication of results and products to a broad range of stakeholders. Communication is in verbal and written form, often using technological solutions for communication. This role will require communication in written and oral form with team members, stakeholders (e.g. other state public health labs, CDC, OIT), as well as the presentation of work at conferences. For example, the results of analyses and designs and execution of cloud infrastructure enhancements will be presented and discussed with team members on a regular basis. The work performed it this role will be submitted to conferences for oral or poster presentations.
Residency Requirement
Minimum Qualifications, Substitutions, Conditions of Employment & Appeal Rights
This posting is open to current of the State of Colorado at the time of submitting your application.
Minimum Qualifications
Experience* Only:
Six (6) years of relevant experience* in the development and maintenance of cloud infrastructure, data science, development and utilization of pipelines for the analysis of genomic data, developing training programs in bioinformatics, developing code, development of infrastructure as code and maintaining proper documentation, or closely related work experience.
OR
Education* and Experience**:
A combination of related education** in Bioinformatics, Computational Biology, Genomics, Computer Science, Cloud Engineering, Data Science, or closely related field and/or relevant experience* in the development and maintenance of cloud infrastructure, genomic data analysis and organization,, developing training programs in bioinformatics, cloud infrastructure, developing code and maintaining proper documentation, or closely related wor an occupation related to the work assigned equal to six (6) years.
Preferred Qualifications And Essential Competencies
Relevant years of State service contribute to a candidate's position-related knowledge, skill, ability, behavior or other posted competency should be considered as a preferred qualification and given weight under the process.
An applicant who has been removed from an employment list or removed from consideration during the selection process may request a review by the State Personnel Director.
As an applicant directly affected by the results of the selection or comparative analysis process, you may file a written appeal with the State Personnel Director.
Review of the completed, signed and submitted appeal will be timely on the basis of written material submitted by you, using the official appeal form signed by you or your representative. This form must be completed and delivered to the State Personnel Board by email at dpa_state.personnelboard@state.co.us within ten (10) calendar days from your receipt of notice or acknowledgement of the Department’s action.
For further information on the Board Rules, you can refer to 4 Colorado Code of Regulations (CCR) 801-1, State Personnel Board Rules and Personnel Director's Administrative Procedures, Chapter 8, Resolution of Appeals and Disputes, at spb.colorado.gov/board-rules .
Supplemental Information
A Complete Application Packet Must Include
Learn more about E-Verify , including your rights and responsibilities.
ADAAA Accommodations : The State of Colorado believes that equity, diversity, and inclusion drive our success, and we encourage candidates from all identities, backgrounds, and abilities to apply. The State of Colorado is an equal opportunity employer committed to building inclusive, innovative work environments with employees who reflect our communities and enthusiastically serve them. Therefore, in all aspects of the employment process, we provide employment opportunities to all qualified applicants without regard to race, color, religion, sex, disability, age, sexual orientation, gender identity or expression, pregnancy, medical condition related to pregnancy, creed, ancestry, national origin, marital status, genetic information, or military status (with preference given to military veterans), or any other protected status in accordance with applicable law. The Colorado Department of Public Health and Environment is committed to the full inclusion of all qualified individuals. As part of this commitment, our agency will assist individuals who have a disability with any reasonable accommodation requests related to employment, including completing the application process, interviewing, completing any pre-employment testing, participating in the employee selection process, and/or to perform essential job functions where the requested accommodation does not impose an undue hardship. If you have a disability and require reasonable accommodation to ensure you have a positive experience applying or interviewing for this position, please direct your inquiries to our ADAAA Coordinator at cdphe_benefits@state.co.us .
Division of Disease Control and Public Health Response
This requires Colorado Residency to apply
This is Hybrid position
We are committed to increasing the diversity of our staff and providing culturally responsive programs and services. Therefore, we encourage responses from people of diverse backgrounds and abilities.
Be BOLD.....Make a REAL difference . . . and join us in serving our communities advancing Colorado's health and protecting the places we live, work, learn, and play, to create a healthy and sustainable Colorado where current and future generations thrive.
Our mission… is to advance Colorado's health and protect the places we live, work, learn, and play.
Our vision… is to create a healthy and sustainable Colorado where current and future generations thrive. In addition to free parking, access to RTD bus lines, Cherry Creek bike path and flexible working arrangements, click the link below to review additional benefits and perks!!! https://cdphe.colorado.gov/careers
Description Of Job
The Division of Disease Control and Public Health Response (DCPHR) is the department’s lead surveillance, planning and response arm for public events including communicable disease outbreaks and epidemics, pandemics, bioterrorism, and other public health and mass casualty events and disasters. The division includes the Office of Emergency Preparedness and Response; State Public Health Laboratory; Health Equity Branch, Communicable Disease Branch; Immunization Branch; Public Health Informatics, Reporting, and Refugee Branch; and Operations Branch. The Division exists to ensure that the Department has the ability to effectively prepare for, monitor, detect, diagnose, investigate, and nimbly respond to all types of conditions, events and disasters that impact the public’s health.
The Work Unit
The work unit exists to provide accurate scientific data and test results about detection, identification, and characterization of microorganisms by current molecular, genomic, and bioinformatic methods in clinical, wastewater, and environmental specimens from culture independent diagnostic tests (CIDTs), as well as following extraction of nucleic acid targets form live cultures, of bacteria, fungi, parasites, viruses, and other agents of public health concern isolated from source specimens. These data are used in timely support of patients’ diagnosis and management, epidemiological investigations of disease outbreaks, rapid response to bioterrorism events, and identification of agents affecting public health and environment.
What You Will Be Doing
The Bioinformatics Cloud Engineer within the public health laboratory oversees developing and maintaining cloud infrastructure, assisting the unit in managing and storing large genomic datasets and bioinformatic analyses, as well as in automating processes such as data storage and pipeline execution. This position is expected to apply state-of-the-art computational and cloud engineering methods and to assist in the development of innovative approaches to cloud infrastructure and software challenges that touch all aspects of NGS data. This includes but is not limited to raw data handling, pathogen identification, outbreak tracking, mapping drug-resistant determinants, development of novel NGS tests, variant analysis, genome annotation, and phylogenetics. Data and analytics involve bacterial, viral, fungal, parasitic, and human NGS data. Cloud engineering experience, coding expertise, efficient communication skills, basic knowledge of microbiology, training, and outreach are necessary requirements for this position.
Development and Maintenance of Cloud Infrastructure
This position builds and maintains cloud-based infrastructure to support large-scale genomic data analysis using Google Cloud Platform (GCP). This includes, but is not limited to, developing and operating robust, scalable, flexible, and secure cloud systems that integrate with bioinformatics analysis platforms (e.g. Seqera, Terra.Bio, AMD platform). This position adheres to and maintains security best practices and assigns appropriate user access permissions for team members and collaborators. Works closely with team members to ensure seamless orchestration of workflows and pipelines and works to automate cloud processes where feasible.
Data Storage and Management
This position oversees maintaining organized data storage and management strategies, adhering to the unit’s data retention and lifecycle policies and works to improve efficiency and cost-effectiveness of storing large scale datasets.
Pipeline Construction, Maintenance, and Execution
Perform bioinformatics data analysis on all NGS data generated in the lab. Responsible for the construction, validation, maintenance, and implementation of bioinformatics pipelines and workflows. Where applicable, move pipelines forward for CLIA validation.
Workforce Development and Consultation
As an ELC AMD Bioinformatics Resource and Training Support Site (BRR/BTL), and AMD Platform IT Security and Privacy Domain Lead (ITSP), significant time is taken to design, construct, and then implement and instruct internal, regional, and national partners. Part of this position will include providing bioinformatics and cloud engineering support to other state public health labs upon request, as well as providing training to other state public health labs through participation in the planning and presentation of instructional materials. Instruction consists of bioinformatics and genomics, but could also include topics of AMD platform implementation, cloud engineering and resource utilization, and large-scale data management and storage. Consultation of regional labs for training and resource implementation is necessary. This role will also participate in ITSP domain activities that include, but are not limited to, consultation with other public health lab partners and CDC on ITSP-related topics, bioinformatics and cloud infrastructure, and user acceptance testing.
Communication
An integral part of work within the unit is communication of results and products to a broad range of stakeholders. Communication is in verbal and written form, often using technological solutions for communication. This role will require communication in written and oral form with team members, stakeholders (e.g. other state public health labs, CDC, OIT), as well as the presentation of work at conferences. For example, the results of analyses and designs and execution of cloud infrastructure enhancements will be presented and discussed with team members on a regular basis. The work performed it this role will be submitted to conferences for oral or poster presentations.
Residency Requirement
Minimum Qualifications, Substitutions, Conditions of Employment & Appeal Rights
This posting is open to current of the State of Colorado at the time of submitting your application.
Minimum Qualifications
Experience* Only:
Six (6) years of relevant experience* in the development and maintenance of cloud infrastructure, data science, development and utilization of pipelines for the analysis of genomic data, developing training programs in bioinformatics, developing code, development of infrastructure as code and maintaining proper documentation, or closely related work experience.
OR
Education* and Experience**:
A combination of related education** in Bioinformatics, Computational Biology, Genomics, Computer Science, Cloud Engineering, Data Science, or closely related field and/or relevant experience* in the development and maintenance of cloud infrastructure, genomic data analysis and organization,, developing training programs in bioinformatics, cloud infrastructure, developing code and maintaining proper documentation, or closely related wor an occupation related to the work assigned equal to six (6) years.
- This experience must be substantiated within the Work Experience section of your application. "See Resume" will not be accepted. In addition, part-time work will be prorated.
- A copy of your transcripts must be submitted at the time of application. Unofficial transcripts are acceptable. Late transcripts will not be accepted.
Preferred Qualifications And Essential Competencies
Relevant years of State service contribute to a candidate's position-related knowledge, skill, ability, behavior or other posted competency should be considered as a preferred qualification and given weight under the process.
- Master’s in bioinformatics, Genomics, Computational Biology, Computer Science, Cloud Engineering or related fields.
- Experience with cloud computing environments, Google Cloud Platform in particular, and Google Cloud services such as DataForm, BigQuery, Dataflow, and Pub/Sub.
- Experience with developing and maintaining Infrastructure as Code (e.g. TerraForm)
- Experience with Cloud platforms used for bioinformatic analysis (e.g. Seqera/Nextflow Tower, Terra.bio) Demonstrated experience in high-throughput sequencing data analysis or method development
- Solid knowledge of Python and/or programming languages and shell scripting.
- Experience working in a Unix/Linux development environment.
- Experience with SQL and using SQL to query large datasets
- Experience using workflow management languages such as WDL and/or Nextflow.
- Experience with containerization technologies to package software and dependencies and development and usage in a cloud computing environment (e.g. Docker, Singularity).
- Experience with version control software including Git and GitHub.
- Experience implementing CI/CD pipelines using tools like GitHub Actions
- Demonstrated experience with bioinformatics applications such as Spades, Skesa, samtools, bwa, minimap2, bedtoolsProkka, Roary, RAxML, Mash, Kraken, AMRfinderPlus.
- Demonstrated experience teaching bioinformatics to a diverse audience.
- Excellent understanding of next generation genomics technologies including Illumina and Oxford Nanopore.
- Knowledge of statistical approaches for analyzing genomic and molecular data in the context of public health and pathogen surveillance.
- Previous experience working in public health is desirable.
- Ability to strategize, organize and plan, including creating and updating training plans
- Ability to effectively communicate both orally and in writing with a wide range of customers
- Excellent critical thinking and problem solving skills.
- Excellent interpersonal and customer service skills.
- Ability to interpret regulations and statutes.
- Ability to interpret and analyze data.
- Keen attention to detail.
- Ability to self-motivate and learn new skills.
- Ability to work well independently as well as in/with a team.
- Ability to collaborate and achieve consensus across work units and programs.
- Pursuant to CDPHE policy, a criminal history background check is required for all positions at CDPHE
- Must be available in the event of an emergency, (e.g., bio-terrorist attack, chemical attack, disease outbreak or all hazards) and be required to report to work immediately at the regular or alternate location. During this time, travel restrictions may be in place.
- Must be available in the event of the activation of the Continuity of Operations Plan (COOP) and be required to report to work immediately at the regular or alternate location. During this time, travel restrictions may be in place.
- On-site position
An applicant who has been removed from an employment list or removed from consideration during the selection process may request a review by the State Personnel Director.
As an applicant directly affected by the results of the selection or comparative analysis process, you may file a written appeal with the State Personnel Director.
Review of the completed, signed and submitted appeal will be timely on the basis of written material submitted by you, using the official appeal form signed by you or your representative. This form must be completed and delivered to the State Personnel Board by email at dpa_state.personnelboard@state.co.us within ten (10) calendar days from your receipt of notice or acknowledgement of the Department’s action.
For further information on the Board Rules, you can refer to 4 Colorado Code of Regulations (CCR) 801-1, State Personnel Board Rules and Personnel Director's Administrative Procedures, Chapter 8, Resolution of Appeals and Disputes, at spb.colorado.gov/board-rules .
Supplemental Information
A Complete Application Packet Must Include
- A completed State of Colorado application.
- If using education to qualify, a copy of your college/university transcripts. Transcripts must be attached to your colorado.gov/jobs application.
- If you are a veteran, a copy of your DD214 attached to your colorado.gov/jobs application.
- All applications that are received by the closing of this announcement will be reviewed against the Minimum Qualifications in this announcement. Candidates who meet the minimum qualifications proceed to the next step.
- Colorado Revised Statutes require that state employees are hired and promoted based on merit and fitness through a comparative analysis process.
- Part of, or all of, the comparative analysis for this position may be a structured application review, which involves a review of the information you submit in your application materials by Subject Matter Experts (SMEs) against the preferred qualifications.
- A top group, up to six candidates, will be invited to schedule an interview with the hiring manager.
Learn more about E-Verify , including your rights and responsibilities.
ADAAA Accommodations : The State of Colorado believes that equity, diversity, and inclusion drive our success, and we encourage candidates from all identities, backgrounds, and abilities to apply. The State of Colorado is an equal opportunity employer committed to building inclusive, innovative work environments with employees who reflect our communities and enthusiastically serve them. Therefore, in all aspects of the employment process, we provide employment opportunities to all qualified applicants without regard to race, color, religion, sex, disability, age, sexual orientation, gender identity or expression, pregnancy, medical condition related to pregnancy, creed, ancestry, national origin, marital status, genetic information, or military status (with preference given to military veterans), or any other protected status in accordance with applicable law. The Colorado Department of Public Health and Environment is committed to the full inclusion of all qualified individuals. As part of this commitment, our agency will assist individuals who have a disability with any reasonable accommodation requests related to employment, including completing the application process, interviewing, completing any pre-employment testing, participating in the employee selection process, and/or to perform essential job functions where the requested accommodation does not impose an undue hardship. If you have a disability and require reasonable accommodation to ensure you have a positive experience applying or interviewing for this position, please direct your inquiries to our ADAAA Coordinator at cdphe_benefits@state.co.us .