Healthcare and Genomics Archives ~ fitzmoskal https://fitzmoskal.me/category/industries/healthcare-and-genomics/ You are _here_ Tue, 05 Mar 2024 20:59:04 +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 Healthcare and Genomics Archives ~ fitzmoskal https://fitzmoskal.me/category/industries/healthcare-and-genomics/ 32 32 11678478 RAG with Offline LLM https://fitzmoskal.me/rag-with-offline-llm/ Tue, 05 Mar 2024 20:59:03 +0000 https://fitzmoskal.me/?p=1755 During my time as Head of Professional Services for a private Genomics based company I spearheaded an initiative to utilise

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During my time as Head of Professional Services for a private Genomics based company I spearheaded an initiative to utilise an open source offline LLM for analysing our Jira, Confluence and Salesforce docs for quick retrieval of process and technical information.

The purpose was twofold,

a) To create a common ‘search’ tool in order to locate a source of truth as to what was configured and where, and

b) To be able to generate process documents very quickly in whole or in part through the use of generative AI.

As these were sensitive company documents, use of a service like ChatGPT was restricted, which is why we opted to trial PrivateGPT with Llama-2-7b amongst other models.

We found RAG to be less than perfect, but it did effectively allow us to search out the right documents. Text generation was better in that we managed to produce good content as an initial template for a process guides, as well as feeding a full process document to generate a RASCI chart. We ran the pilot service on AWS EC2 infrastruture.

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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

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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

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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

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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.

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Egyptian Genomics Institute – Software Delivery https://fitzmoskal.me/egyptian-genomics-institute-software-delivery/ Mon, 26 Feb 2024 20:04:01 +0000 https://fitzmoskal.me/?p=1487 Software Delivery I managed the team that took part in a deployment of genomics analysis software to a government programme

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Software Delivery

I managed the team that took part in a deployment of genomics analysis software to a government programme based in Cairo Egypt worth £2m in total, I also acted as a hands-on technical lead.

I managed the resourcing of a consultant from China to attend for 3 weeks and had scheduled to be there on the first week. The deployment was time-sensitive and had to be completed on-premise in this window as we wouldn’t have remote access.

The consultant from China was delayed, so I had to use my technical skills to quickly get the install going having not performed one before. I did alone on the first day – a Sunday – and then brought in my other consultant and a DevOps resource on conference call for the following two days, until the Chinese consultant arrived. All this took place whilst the client was monitoring over my shoulder – so I had to present confidence in what I was doing at the same time. The software was successfully deployed inside of the 3 weeks. However there were some performance issues identifed.

Health Check

After concerns were raised by the client regarding performance – with accusations flying, I took the decision to prepare a mirror environment in our offices and we requested soem of their sample files to process and confirm that the software was capable of processing them – which it was. So the issues pointed to infrastructure.

I agreed to attend site with one of the product managers to perform a health check against the software and hardware. I had some input in what to look for from the DevOps team, but largely had to script the health check myself against Kubernetes, NFS and PostgreSQL. Onsite, I ran multiple tests and perfected the script which used a combination of tools including kubectl, docker, fio, iostat, mtr and netstat. With this I was able to narrow down the issue to packet loss between the application and NFS, which was hosted on a different network split by a switch or router – which was not as specified in the Solution Design we had outlined.

This helped to not only provide the customer with confidence in the solution and our commitment to support, but did prevent them from walking away from the contract as they had previously disputed ownership of the issue.

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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

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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.

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Healthcare Company – AIOps https://fitzmoskal.me/healthcare-company-aiops/ Mon, 26 Feb 2024 17:29:05 +0000 https://fitzmoskal.me/?p=1475 I worked in presales to present insights into their ITSM operations gathered from Talos back to the client. My involvement

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I worked in presales to present insights into their ITSM operations gathered from Talos back to the client. My involvement was in data cleansing and preparation for injesting into Talos for supervised and unsupervised learning. Once Talos had created the reports, I would then import these to PowerBI to develop the insights. With AI we were able to identify:

  • Issue candidates for automation e.g. “password reset”
  • Lack of categorisation and service catalogue, poor summaries written in tickets
  • 3rd party structured automation information posted into notes fields
  • Categorical data located in unstructured notes fields
  • Under-utilisation of knowledge
  • Change requests logged as tickets leading to high level of tickets with low MTTR
  • High level of critical abnormalities requiring problem RCA
  • General lack of granularity in categories, impacting management reporting

This was followed up with an offer to the client to deliver the recommendations such as service desk training, restructuring categories, data cleansing, and knowledgebase improvements

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Sample Sizing https://fitzmoskal.me/sample-sizing/ Mon, 19 Feb 2024 20:40:21 +0000 https://fitzmoskal.me/?p=1145 A small script utilising scikit-learn for predicting the size of a build of Congenica on-premise given the number of genome

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A small script utilising scikit-learn for predicting the size of a build of Congenica on-premise given the number of genome samples to process.

https://github.com/codefitz/sample-sizing

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