Bioinformatics Archives ~ fitzmoskal https://fitzmoskal.me/tag/bioinformatics/ You are _here_ Thu, 29 Feb 2024 16:10:14 +0000 en-GB hourly 1 https://wordpress.org/?v=6.9.4 https://fitzmoskal.me/wp-content/uploads/2024/02/cropped-result_880649-32x32.jpeg Bioinformatics Archives ~ fitzmoskal https://fitzmoskal.me/tag/bioinformatics/ 32 32 11678478 VCF File Validation https://fitzmoskal.me/vcf-file-validation/ Mon, 26 Feb 2024 21:08:20 +0000 https://fitzmoskal.me/?p=1497 This script was bourne of necessity to validate VCF files for injestion into Congenica. The platform does it’s own validation

The post VCF File Validation appeared first on fitzmoskal.

]]>
This script was bourne of necessity to validate VCF files for injestion into Congenica. The platform does it’s own validation but the output in case of error is not human-friendly. This directs the user to which line in the VCF file might be at fault.

https://github.com/codefitz/vcf_validation

The post VCF File Validation appeared first on fitzmoskal.

]]>
1497
Genomics Laboritory – Export Service https://fitzmoskal.me/genomics-laboritory-export-service/ Mon, 26 Feb 2024 20:16:08 +0000 https://fitzmoskal.me/?p=1492 As Head of Professional Services I developed and introduced a new billable service for customers which allowed them to receive

The post Genomics Laboritory – Export Service appeared first on fitzmoskal.

]]>

As Head of Professional Services I developed and introduced a new billable service for customers which allowed them to receive monthly or quartery exports of analysed sequence data for their use in predicting trends.

This involved the export of large sequenced data in the form of VCF SNV files. I managed the project team which included a Project Manager, Bioinformatics Consultant, DBA and DevOps in order to ensure the first customer was properly onboarded and that the customer would receive notifications when the data export was ready.

The post Genomics Laboritory – Export Service appeared first on fitzmoskal.

]]>
1492
NHS Genomics Partner – Integrations & Software Development https://fitzmoskal.me/nhs-genomics-partner-integrations-software-development/ Mon, 26 Feb 2024 19:31:19 +0000 https://fitzmoskal.me/?p=1484 As Head of Professional Services I took over responsibility for a number of software integrations written by a bioinformatics consultant

The post NHS Genomics Partner – Integrations & Software Development appeared first on fitzmoskal.

]]>

As Head of Professional Services I took over responsibility for a number of software integrations written by a bioinformatics consultant who had previously left the company. One of these integrations was supplied to a parnter organisation and had been reported to have an undetected design flaw which raised a ‘highest severity’ ticket. No-one in my team was familiar with the code, so I had to reach out and coordinate with DevOps and Engineering for assistance.

Through bargaining and persistance I secured some time of one of the lead bioinformaticians to take a look at the code, review the clients requirements and make the changes. This was the easiest part – I recognised the issue with the code myself, but as I wouldn’t understand the genomics interpretation part, I did not want to make edits myself. The second part of the issue was with clinical decisions that had already been made with the flawed code. There was little that I could do here, but it was down to me to make sure that the right resources were aware and assigned to figure out which decisions had been impacted to report back to the client.

The code fix was done within SLAs, finding the impacted clinical decisions took longer. My final action was to ensure that the application was correctly documented for future support and ensure that the client sign off on the new implementation of the code (to ensure that there is record of agreement that it now worked as expected – which was missing before).

I was also engaged with this partner through organising a resource to work on custom reporting, using a combination of python and flask. I acted as liaison and project manager with the customer ensuring that the code was developed to specification and that milestones for delivery, test and sign off were met.

The post NHS Genomics Partner – Integrations & Software Development appeared first on fitzmoskal.

]]>
1484