Bioinformatics Platform Options for Public Health Laboratories

Joel R Sevinsky, PhD

Bioinformatics Consultant, Northeast Region

Disclosure

I report the following financial relationships or relationships to products or devices I or my spouse/life partner have with commercial interests related to the content of this APHL supported and P.A.C.E. accredited activity:

• Principal to Theiagen Consulting LLC

Bioinformatics Platforms Discussed Today

• Commercial• Bionumerics (www.applied-maths.com/bionumerics)

• CLC Genomics Workbench (www.qiagenbioinformatics.com/products/clc-genomics-workbench/)

• Web-based resources• Galaxy Server (usegalaxy.org and galaxytrakr.org)

• Center for Genomic Epidemiology (www.genomicepidemiology.org)

• NCBI Pathogen Detection Browser (www.ncbi.nlm.nih.gov/pathogens)

• EDGE Bioinformatics (edgebioinformatics.org)

• Linux Command Line Interface (CLI)• On premise – like buying a home

• Cloud based – like leasing a home month to month• Amazon Web Services – AWS (aws.amazon.com)

• Google Cloud Platform – GCP (cloud.google.com)

• Microsoft Azure (azure.microsoft.com)

Disclosure #2

There is LOTS of overlap between the three categories of platforms we will discuss and demo. I will be making some overly broad generalizations.

Commercial Platform

Advantages• Complete platform with GUI.

• Often can be run on an off the shelf PC with decent RAM and CPU.

• Most companies have a small army of software developers supporting the software.

• Some have data management capabilities.

• Don’t need to be a bioinformatician to run.

• Most IT departments will have fewer security concerns since it is usually run on internal hardware.

Disadvantages• Not as customizable.

• Don’t always know the exact parameters used for an analysis.

• Some don’t have data management capabilities.

• Some don’t have data sharing capabilities between locations.

• Innovation occurs on the vendors timeline.

• Vendors business priorities may change.

Web-based Platform

Advantages• Don’t need an investment in software or capital since these are often cloud based and many are free.

• Frequently project specific tools are available.

• Web-based GUI for ease of analysis.

• Can be accessed from anywhere.

• Inexpensive and actively supported.

Disadvantages• Often not amenable to metadata sharing.

• IT fear of cloud-based system.

• Not as customizable.

• Often free tier requires sharing with the public.

• Often you are dependent on the developers to continue developing.

Linux CLI

Advantages• Total control and full customization of your bioinformatics platform.

• Full access to open source tools for bioinformatics.

• Share your pipelines with anyone.

• Connect to and move data between cloud resources.

• Extremely flexible, especially during an investigation.

Disadvantages• Need some bioinformatics knowledge to implement or a bioinformatician.

• Bioinformaticians are not software developers.

• Security concerns based on where the CLI environment is hosted.

• IT restrictions for root access.

Which to choose?

• Unfortunately, many times the decision is made for you.• Budget constraints on hardware/capital expenditures.• IT restrictions on Linux systems.• IT restrictions on cloud computing.• IT restrictions on duties (as in who maintains the system).

• Purchasing restrictions on vendors.• HR restrictions on qualified personnel (can’t pay to play).

Demo Time

• Bionumerics – Logan Fink

• Web-based – Kevin Libuit

• Linux CLI on premise – Kelly Oakeson