nkrumm

I've been in demo rooms that priced in about $100-300k (~2015 dollars), and those sound remarkably close. Not all sound/bands can be reproduced, and it really depends on the recording. Could you do it for less, also? Probably. But it was pretty fun to hear the highest end.

UW Laboratory Medicine | ONSITE (Seattle, WA) or REMOTE (US-based only) | Full-Time |

Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 1200 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for:

* Bioinformatics developer * within our NGS analytics team and laboratory. We're looking for someone to develop and operationalize our NGS data processing pipelines, build out our operational tools/databases/systems, as well as investigate new opportunities in a translational in long-read sequencing and cell-free DNA sequencing. Experience with bioinformatics tools, annotation databases, common bioinformatics file formats highly valued. You will be working in a team of 5+ bioinformatics developers, and interacting closely with a full-stack engineering team, laboratory staff and directors.

If this sounds interesting please reach out at nkrumm@gmail with a resume. I will do my best to get back to you.

im not an expert, but take a look at the llamaindex structured data retrieval examples: https://docs.llamaindex.ai/en/stable/understanding/putting_i...

There are also examples that combine semantic retrieval and structured retrieval.

I had the urge to try this out a while back, here's what I came up with: https://gist.github.com/nkrumm/2b154ea2041511233079222373c83...

The decorator invokes AI completion only the first time the function is run.

edit: I lost interest before I was able to get arguments to work ¯\_(ツ)_/¯

UW Laboratory Medicine | ONSITE (Seattle, WA) or REMOTE (US-based only, sorry) | Full-Time

Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for:

* TWO Full Stack Developers * to support our clinical laboratories. Build tools to improve our operation efficiency, automation and capabilities for our clinical labs. In particular, we are looking to built out the tooling and increase efficiency in our main clinical labs. You'll be working to improve physical workflows (samples in lab) via faster applications, more relevant and more accessible data sources, and (future) integration of novel technologies such as RFID.

These roles are about 50% full-stack web development (Flask and React preferred technology), 20% Infra/cloud engineering (AWS), and 30% team immersion (strong verbal + design skills needed).

Work environment: Flexible work/remote schedule, excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting please reach out at [email protected] with a resume. Our recruitment team will do my best to get back to you.

Thanks, Nik.

Are there any projects that are targeting enterprise/business use cases? I would love to have:

  - a ChatGPT web ui (like chatbot-ui), 
  - but server side and (self-)hosted 
  - and with our own SSO auth. 
  - Bonus points for including Azure OpenAI endpoint connectivity + auditing/logging by user.

edit formatting

We did something like this, by using postgresql's `set_config()` before every transaction. The trigger functions can read that value using `current_setting()`. It works for us, but for a relatively low-traffic internal application.

UW Laboratory Medicine | ONSITE (Seattle, WA) or REMOTE (US-based only, sorry) | Full-Time Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for:

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and operationalize our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

* Senior Full Stack Developer(s) * to support our clinical laboratories. Build tools to improve our operation efficiency, automation and capabilities for our clinical labs. This role is about 50% full-stack web development (Flask and React preferred technology), 20% Infra/cloud engineering (AWS), and 30% team immersion (strong verbal + design skills needed).

* Data Engineer and Integration Engine Developer * to support our HL7 and clinical data interfacing systems. We use the Iguana interface engine to route data from laboratory instruments to connected systems. Must have a love for data munging and making connections between systems highly reliable. Experience with Epic, HL7/FHIR or other healthcare data exchange formats desired but not required.

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting please reach out at nkrumm@gmail with a resume. I will do my best to get back to you.

Thanks, Nik.

UW Laboratory Medicine | ONSITE (Seattle, WA) or REMOTE (US-based only, sorry) | Full-Time

Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for:

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and operationalize our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

* Senior Full Stack Developer(s) * to support our clinical laboratories. Build tools to improve our operation efficiency, automation and capabilities for our clinical labs. This role is about 50% full-stack web development (Flask and React preferred technology), 20% Infra/cloud engineering (AWS), and 30% team immersion (strong verbal + design skills needed).

* Data Engineer and Integration Engine Developer * to support our HL7 and clinical data interfacing systems. We use the Iguana interface engine to route data from laboratory instruments to connected systems. Must have a love for data munging and making connections between systems highly reliable. Experience with Epic, HL7/FHIR or other healthcare data exchange formats desired but not required.

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting please reach out at nkrumm@gmail with a resume. I will do my best to get back to you.

Thanks, Nik.

UW Laboratory Medicine | ONSITE/REMOTE (Seattle, WA) | Full-Time

Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for:

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and operationalize our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

* Senior Full Stack Developer * to support our clinical laboratories. Build tools to improve our operation efficiency, automation and capabilities for our clinical labs. This role is about 50% full-stack web development (Flask and React preferred technology), 20% Infra/cloud engineering (AWS), and 30% team immersion (strong verbal + design skills needed).

* Data Engineer and Integration Engine Developer * to support our HL7 and clinical data interfacing systems. We use the Iguana interface engine to route data from laboratory instruments to connected systems. Must have a love for data munging and making connections between systems highly reliable. Experience with Epic, HL7/FHIR or other healthcare data exchange formats desired but not required.

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting please reach out at nkrumm@gmail with a resume. I will do my best to get back to you.

Thanks, Nik.

Here is the actual draft of the recommendation as well as supporting evidence: https://www.uspreventiveservicestaskforce.org/uspstf/recomme...

Edit: Here's the document that actually outlines "what changed" from 2016 to the current draft: file:///Users/nkrumm/Downloads/aspirin-use-cvd-prevention-draft-modeling-report.pdf

side project idea: create a bot that takes a screenshot of all new Show HNs, and post a comment to the thread with the screenshot

UW Laboratory Medicine | ONSITE/REMOTE (Seattle, WA) | Full-Time Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging. Currently recruiting for:

* Senior Interface/Integration Engine Developer * to support our HL7 and clinical data interfacing systems. Experience with SunQuest, Epic, the Lua programming language, HL7/FHIR or other healthcare data exchange formats desired. (Please apply here: https://uwhires.admin.washington.edu/eng/candidates/default....)

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting...

1) Please apply via the UW HIRES website (Link above)

2) reach out at nkrumm@gmail with a resume.

Thanks, Nik.

UW Laboratory Medicine | ONSITE/REMOTE (Seattle, WA) | Full-Time Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

Currently recruiting for several roles

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and operationalize our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

* Full Stack Developer * to support our clinical laboratories. Build tools to improve our operation efficiency, automation and capabilities for our clinical labs. This role is about 50% full-stack web development (Flask and React preferred technology), 20% Infra/cloud engineering (AWS), and 30% team immersion (strong verbal + design skills needed).

* Senior Interface/Integration Engine Developer * to support our HL7 and clinical data interfacing systems. Experience with SunQuest, Epic, the Lua programming language, HL7/FHIR or other healthcare data exchange formats desired.

Our stack: Primarily Python, Nextflow, and React/PostgreSQL. PHI-compliant AWS cloud infrastructure with push-to-deploy application servers and a batch-processing pipeline.

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting...

1) Please apply via the UW HIRES website. The jobs above are: - https://uwhires.admin.washington.edu/eng/candidates/default.... - https://uwhires.admin.washington.edu/eng/candidates/default.... - https://uwhires.admin.washington.edu/eng/candidates/default....

2) reach out at nkrumm@gmail with a resume.

Please note-- At this time we cannot support fully-remote (i.e., not in greater Seattle area) applicants or those needing visas.

Thanks, Nik.

UW Laboratory Medicine | ONSITE (Seattle, WA) | Full-Time

Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and maintain our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with germline specific bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

Our stack: Primarily Python, Nextflow, and React/PostgreSQL. PHI-compliant AWS cloud infrastructure with push-to-deploy application servers and a batch-processing pipeline.

Work environment: Flexible work/remote schedule (currently fully remote for COVID), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will absolutely impact the health and lives of those patients.

If this sounds interesting... 1) Please apply via the UW HIRES website at: https://uwhires.admin.washington.edu/eng/candidates/default.... 2) reach out at nkrumm@gmail with a resume.

Please note-- At this time we cannot support fully-remote (i.e., not in greater Seattle area) applicants or those needing visas.

Thanks, Nik.

Ah you are right. It was still great :)

I remember seeing an ad for the 4x200 mhz system on the back page of a MacMall catalog and nearly falling off my chair. At the time we had a LCII, with 25 MHz and a maxed out 8mb ram. The thought of a eight hundred MHz was incredibly astounding— few things ha e matched that level of astonishment since.

UW Laboratory Medicine | ONSITE (Seattle, WA) | Full-Time Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and maintain our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with germline specific bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

Our stack: Primarily Python, Nextflow, and React/PostgreSQL. PHI-compliant AWS cloud infrastructure with push-to-deploy application servers and a batch-processing pipeline.

Work environment: Very flexible work/remote schedule (currently fully remote), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will impact the health and lives of those patients!

Please reach out at nkrumm@gmail with a resume if interested. At this time we cannot support fully-remote (not in PNW) applicants or those needing visas.

Thanks, Nik.

UW Laboratory Medicine | ONSITE (Seattle, WA) | Full-Time Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics in genomics, mass spectrometry, flow cytometry and automated imaging.

* Bioinformatics developer * within our NGS laboratory. We're looking for someone to develop and maintain our germline NGS data processing pipelines, as well as investigate new opportunities in a translational research context. Experience with germline specific bioinformatics tools, annotation databases, common bioinformatics file formats highly valued!

Our stack: Primarily Python, Nextflow, and React/PostgreSQL. PHI-compliant AWS cloud infrastructure with push-to-deploy application servers and a batch-processing pipeline.

Work environment: Very flexible work/remote schedule (currently fully remote), excellent UW benefits, cross-sectional work environment where you will be working with technologists, trainees, physicians and laboratory directors. The UW maintains a "Patients are First" model of operation-- your contribution at UW Laboratory Medicine will impact the health and lives of those patients!

Please reach out at nkrumm@gmail with a resume if interested. At this time we cannot support fully-remote (not in PNW) applicants or those needing visas.

Thanks, Nik.

Not cynical. Also, academic institutions take "overhead" from grants, sometimes up to 100%, ostensibly to provide infrastructure, keep the lights on, etc. (this means the $5m grant from NIH for the researcher really costs the NIH $10m).

"cores" in an academic setting refer to shared institutional resources, e.g. for DNA (or other) sequencing, mass spectrometry, computing resources, cell lines, etc.

This sort of rapid test (say, results in under 4 hours from collection) is useful in a few different acute situations:

- Patients needing emergent surgery while also presenting with symptoms concerning for COVID-19.

- Critical healthcare workers (physicians, nurses needing rule out and rapid return to work)

- Patients presenting who may have contributed to exposure of other high risk individuals (to speed up time of tracing)

Your other points are valid.

It boils down to people, logistics, and efficiency:

Yes, we can produce the primers, develop the tests, ramp up the supply of RNA extraction kits, swabs, tips, etc. Individually easy, but together more challenging, especially when the entire world is also trying to acquire the same products.

Yes, large, fast and high-scale instruments exist. But, they need to be set up and calibrated. They need adequate power, cooling, water, space, etc. The technicians need training. They need network interfaces, etc.

Yes, it's a simple test. But there are still SO MANY steps needed to generate a result from a sample, and those take people. Just looking at the laboratory workflow: 1) Sample received in shipment -- unbox, scan manifest (if provided) 2) Unbag sample + requisition 3) Check sample label (usually handwritten) and verify accuracy to requisition (possibly handwritten). In an ideal case, orders are coming in as "interfaced orders" (meaning electronically) but many smaller clinics/hospitals will not have this. 4) Enter all demographics of the patient into laboratory system 5) Have second person verify the information 6) Re-bag and send sample to location in lab with test instrumentation 7) Technicians unbag, verify label + order accuracy 8) Decant sample from non-standardized tube sent to lab to standard tube used in lab 9) Scan into liquid handling robot... ...et cetera, et cetera

As I will probably find out in the replies there are "solutions" to all of these problems, and many labs utilize them. However, to scale such a complex system so quickly means that there is no room for a "test environment", and all changes have to be made "in production". Even simple changes to the workflow require days of prep to communicate to all of the staff across three daily shifts-- you get the idea.

source: i'm a laboratory medicine resident at the UW lab. We scaled from 0 to 3000 tests in 2 weeks and it's been an incredible all-hands effort.

The commercially available BioFire panel tests for regular coronavirus, NOT SARS-CoV-2 (the virus responsible for Covid-19). They may have something in the works. that said, these machines are not very high throughput; more of a point of care test for small/medium hospitals.

The Hologic Panther Fusion is another automated open platform.

The decision to lock people is for FDA approval. FDA approval means more labs can run your test and reimbursement is more of a sure thing.

The video above (at least one of them) was showing an entire automation line built on Roche technology-- easily an order of magnitude more than 400k. The Cobas 8800 is just a component of that entire line.

Everyone is welcome to take their own health into their own hands. However, for others looking to this as advice, please be aware that:

1) ACE inhibitors (lisinopril, etc.) are generally though to be enzymatic inhibitors of ACE, not ACE2 [1]. Also, enzymatic inhibition of the enzyme does not mean that it will prevent a virus from using that protein as an entry mechanism.

2) Chloroquine is an old drug with a well known safety profile, but it is certainly not a "safe" drug-- there are many known side effects including life threatening or severely disabling ones. As an MD, I recommend always consulting with your own medical provider(s) before starting any medications.

[1] e.g., https://www.ncbi.nlm.nih.gov/pubmed/15897343