Projects

Bioinformatics

Submitted a study and the reviews came back asking for in depth sequencing? Now you need to choose what you are going to do. Genomics? Transcriptomics? Proteomics? What kind? Whole genome? Whole Exome? Bulk or single-cell? Does your RNAseq capture miRNA? Is the read-length long enough to capture rare variants?

Doing sequencing for the sake of doing sequencing is not a good strategy. Let us help you cut through the noise and determine the kind you need that will give biologically relevant answers.

Data Science

Extensive experience deciphering the data to get answers. For an example dose-response modelling project:

Dose Control Treatment
0 100 100
0 97 96
0 104 100
0 97 101
0 105 99
0 103 101
0 103 104
0 104 102
1 100 100
1 97 104
1 104 99
1 100 99 


Estimated effective doses

       Estimate Std. Error    Lower    Upper
e:1:10  12.8685     1.5614   9.7442  15.9928
e:1:50  80.5518    17.8117  44.9106 116.1929

Estimated effective doses

         Estimate Std. Error      Lower      Upper
e:1:10 1.2687e+00 5.8843e-01 9.2112e-02 2.4454e+00
e:1:50 1.2418e+03 2.3918e+02 7.6357e+02 1.7201e+03

Lab Efficiency

Do you have a great idea for a novel therapy or biotech application, but it seems to go nowhere? Often this is due to disorganization in the lab; be it the chemical cabinet, ultracold freezer, or desktop filesystems. It become hard to find things and that ends up frustrating team members as each develops their own enclosed way of keeping what they need organized – at the expense of the team. We provide audits of smaller labs or those labs that have not implemented good organizational practices before. We can identify painpoints and help you eliminate the friction that is slowing your progress.

Reproducibility

For academic labs and startup, the initial focus may not be on industry standard reproducibility. To be honest, the technology seems to change weekly on what is best practice. CoreBioPathways can help create robust data pipelines: including data collection, data storage, data visulaization, data interpretations, journal articles, references, validation, etc.

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Technology

Do you remember the last time you decided on software or hardware? On the very operating system that your lab uses? Perhaps you looked into linux 15 years ago and decided that system was too complicated. It might be time to take another look and see what has happened in the years since; the usability, the tools, the compute power. CoreBioPathways can help you navigate these systems, and even customize different flavors of linux to your specific needs. The best part? The OS is free, as are most of the software tools, and there is a robust developer community pushing the quality bar higher everyday.

Consumables/Equipment Audit

Did you know some common laboratory consumables have increased in price 400% since 2020? Are you able to pinpoint the last time your lab evaluated your needs? Have they changed in the last 5 years? The last year? The last month? Wouldn’t it be better to be able to pinpoint where every consumable in your lab lives, how often it is used and how important it actually is? We can help you do this, find where money is wasted or would be put to better use.

Subject Matter Expertise

Expertise in

  • Microbiology
    • Bacterial
      • Pathogensis
      • Genomics - Transcriptomics - Proteomics
      • Fermentation
  • Oncology
    • Cell and gene therapy treatments
  • Molecular biology
    • Assays
    • Electrophoresis
    • PCR/qPCR/RTPCR
    • Sample preparation
    • Kit troubleshooting
    • Protein Design - Production - Purification - Assessment
    • Vector design - Viral - plasmid - other
  • R & Python Programming - Linux/Unix/Bash/Shell
  • Application Design - Shiny - Dash
  • 5 years oncology and cell-and-gene therapy