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bruth

444 karma · joined October 23, 2009

[ my public key: https://keybase.io/byronruth; my proof: https://keybase.io/byronruth/sigs/5iuOn3dmbf20FOk4L1qozdO6haGTff4ITploibnfhys ]

meet.hn/city/us-Allentown

Socials: - x.com/thedevel - github.com/bruth

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bruth··on A cryptography game-changer for biomedical research at scale
Nice application of HME. The runtime is pretty long especially if there are faults (which is not talked about). Also it is a big assumption that each institution will have equal sized data. That is never the case in practice, so inevitably there will be a hot spot.

The other hurdles they mentioned:

  * data prep and transfer
  * harmonization of the data model
are still hurdles for many institutions. The second one in particular although standards like FHIR and OMOP are increasing traction. Other data modalities like imaging would be more difficult.
bruth··on Ask HN: Who is hiring? (September 2021)
Hrm. It shouldn't be instantly denied, do you mind emailing me your resume and I will talk to my HR rep to see what is up?
bruth··on Ask HN: Who is hiring? (September 2021)
The Children's Hospital of Philadelphia | Software engineer | Philadelphia, PA | Full-time | Remote/Onsite

This role will work with a team of software engineers and bioinformatics scientists focused on architecting and implementing optimized data services, interfaces, and integrations for ‘omics data (genomics, proteomics, etc).

We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge. Existing bioinformatics knowledge is not required as long as you are willing to learn!

Apply: https://careers.chop.edu/job/Philadelphia-'Omics-Softwa...

If you have questions or would like a more direct overview of the position, please feel free to reach out ruthb [at] chop [dot] edu.

bruth··on Kafka without ZooKeeper
The author now works at Confluent.
bruth··on Kafka without ZooKeeper
There was a more recent 2.2 release with durable streams [0]. There is also a comparison page including Kafka [1].

[0]: https://docs.nats.io/whats_new_22 [1]: https://docs.nats.io/compare-nats

bruth··on Show HN: Caddy 2
The REST API for dynamic updates is attractive. Was it influenced by Envoy? Are there any influences/overlap with Envoy? Is Caddy overlapping in the space of Envoy in any notable way?

I will say that getting started with and learning the configuration landscape of Envoy is quite painful, so the simplicity and approachability of Caddy has always been attractive.

bruth··on Ask HN: Who is hiring? (April 2020)
The Children's Hospital of Philadelphia | Bioinformatics software engineer | Philadelphia, PA | Full-time | Onsite (However, Remote now and for the coming months..)

The Children’s Hospital of Philadelphia (CHOP) Research Institute and its Dept of Biomedical and Health Informatics (DBHi) are seeking a software engineer to help build an enterprise-level data and informatics platform called “Arcus”. The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan, high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.

This role will work with a team of bioinformatics scientists, software engineers and genomics faculty focused on architecting and implementing a cloud-native platform to support storing and analyzing enterprise wide genomic data including data management, harmonized pipelines, and variant warehouse components. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

Apply: https://careers.chop.edu/job/Philadelphia-Bioinformatics-Eng...

If you have questions or would like a more direct overview of the position, please feel free to reach out ruthb [at] chop [dot] edu.

bruth··on Programming Models for Distributed Computation
What does writing in Markdown have to do with the complexity of the topic? Heather Miller is an assistant professor at CMU and well respected and certainly an expert in this context. Clearly she believed Markdown was sufficient for her purpose and/or wanted to leverage the other benefits beyond just its simplicity. Did you see that book is being rendered on a site? http://dist-prog-book.com/chapter/2/futures.html
bruth··on Google Cloud Next 2020 – in person event cancelled
Yes it is a "spin" and yes technically the "in person" component is canceled (but who knows how they will emulate the hallway tracks)... but frankly this is a responsible change.
bruth··on Ask HN: Who is hiring? (February 2020)
The Children's Hospital of Philadelphia | Bioinformatics software engineer | Philadelphia, PA | Full-time | ONSITE

The Children’s Hospital of Philadelphia (CHOP) Research Institute and its Dept of Biomedical and Health Informatics (DBHi) are seeking a software engineer to help build an enterprise-level data and informatics platform called “Arcus”. The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan, high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.

This role will work with a team of bioinformatics scientists, software engineers and genomics faculty focused on architecting and implementing a cloud-native platform to support storing and analyzing enterprise wide genomic data including data management, harmonized pipelines, and variant warehouse components. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

https://careers.chop.edu/job/Philadelphia-Bioinformatics-Eng...

bruth··on Show HN: An experimental distributed SQL database from scratch in Go
If it is intended to be a reference project, I suggest focusing on writing the README sections first highlighting the main areas and then linking to code sections to ease the navigation.

You may or may not be aware, but Andy Pavlo records his courses and puts them on YouTube. His latest playlist covers the main database topics with the last five or so lectures covering distributed databases: https://www.youtube.com/playlist?list=PLSE8ODhjZXjbohkNBWQs_...

edit: ^suggesting Pavlo's work since he introduces database concepts very well, so it may be worth structuring the reference architecture in the same way.

bruth··on Layered Programming (2013)
Posted in 2013
bruth··on Sketchviz – Graphviz graphs in a hand-drawn style
> this is really just stringing a bunch of existing tools together

This is essentially what all developers do to varying degrees. The whole is greater than the sum of its parts!

bruth··on Microsoft launches new open-source projects around Kubernetes and microservices
> Stop the error!

I know this is rhetorical, but I've been bitten by this enough times so for those who don't know `no` will translate to a boolean false.

bruth··on Ask HN: Who is hiring? (October 2019)
The Children's Hospital of Philadelphia | Bioinformatics engineer | Philadelphia, PA | Full-time | ONSITE

The Children’s Hospital of Philadelphia (CHOP) Research Institute and its Dept of Biomedical and Health Informatics (DBHi) are seeking a software engineer to help build an enterprise-level data and informatics platform called “Arcus”. The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan, high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.

This role will work with a team of bioinformatics scientists, software engineers and genomics faculty focused on architecting and implementing a cloud-native platform to support storing and analyzing enterprise wide genomic data including data management, harmonized pipelines, and variant warehouse components. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

https://careers.chop.edu/job/Philadelphia-Bioinformatics-Sof...

bruth··on Tiler: Build Images with Images
I actually thought the same thing. I thought this was a tool to compose Docker images transparently in some way.
bruth··on A Bid to Maintain One of the World’s Oldest Culinary Traditions
My comment adds no value to the thread but are you really applying the concept of software licenses to an eatery? This is a classic technique for generating buzz and demand. Many many restaurants do it. People are fine with it, no harm is done. It does not violate any rights. Owners can choose to serve whom they please.
bruth··on Scaling NSQ to 750B Messages (2016)
Note this is from 2016
bruth··on What Does a Software Development Manager Do Next?
> I find myself not adding any value to the team.

If the team is as optimized as it can be, then it may be time to move on from this team to another where you can add value. This sounds like an obvious statement, but without knowing much about your organization this may or may not be a viable option.

But again to my original, what do you want to do? How do you want to grow? What impact do you want to have? If you have the organization structure such that you can make a case to join a new team and help them grow and/or help with strategy for the organization as a whole (which will touch multiple teams), then there is that path as well.

If you want to transition organizations altogether then the above still holds.. in the sense that you need to define your own goals and then find an organization where you can develop them and have an impact.

bruth··on What Does a Software Development Manager Do Next?
Where do you want to go? It sounds like you are implying you want to get back to the technical work? If the job does not allow, then you may need to find a role. Or is the concern that you are losing touch with the current tech and can't make technical decisions like you used to? Or are you asking what is the next step as a technical manager?

If you feel that you aren't good at anything (which clearly is not true given that you've fostered your team) then what is it that you want to get good at?

bruth··on Ask HN: Who is hiring? (August 2019)
The Children's Hospital of Philadelphia | Software engineer | Philadelphia, PA | Full-time | ONSITE

Seeking a software engineer to help build an enterprise-level data and informatics platform called “Arcus”. The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan, high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.

This role will work on a small team focused on architecting and implementing a cloud-native platform that supports the goals of the Arcus program. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

More details: https://careers.chop.edu/job/Philadelphia-Software-Engineer-...

bruth··on Ask HN: When does it make sense to roll your own X?
I second this approach which is what I do as well. My baseline is that I prefer to not have any dependencies. This is usually not realistic nor necessarily pragmatic in practice (i.e. reinventing a relational database), but its a good baseline.

My general feeling towards dependencies (in programs or life) is "do I really want to depend on this thing?" Almost always the answer should be "no". But the follow-up is "do I really need to depend on this thing?" and sometimes the answer is yes because I don't want to or can't re-implement the thing due to time or because I don't have the expertise.

bruth··on Show HN: Web pages stored entirely in the URL
In this context, you are implying the platform is the browser? Assuming you produce your own content and own the domain for which these URLs are being produced then, yes you are left to trust the clients that actually render the content.
bruth··on Use links not keys to represent relationships in APIs
This argument is true for any data that was included in the response. If the client chooses to cache it, it needs to deal with it being stale.. which in this case could result in a 404. Obviously it would be a nice-to-have if the server had a redirect from the old to new.

> Even if you figured all of that out, links are not idiomatic if your users consume your api via an RPC or GraphQL.

Agreed, although you could model a link in the object-based structure representation to match the protocol, something like..

  # RPC
  {
    "rel": "owner",
    "procedure": "GetOwner",
    "args": {
      "id": 98765
    }
  }

  # GraphQL
  {
    "rel": "owner",
    "root": "owner",
    "args": {
      "id": 98765
    }
  }
bruth··on Ask HN: Who is hiring? (May 2019)
The Children's Hospital of Philadelphia | Data Engineer | ONSITE (Philadelphia) | Full-time

The Children’s Hospital of Philadelphia (CHOP) Research Institute is building a data and informatics platform called “Arcus” whose core goal is to link clinical and biological data in order to enable solving the most challenging problems in child health.

I am the one hiring, so feel free to reach out to me directly first if you any questions: ruthb@chop.edu

https://careers.chop.edu/job/Philadelphia-RIA-Programmer-II-...

bruth··on Event Sourcing is Hard
Event sourcing is often described in the context of a rich domain model where every event has slightly different semantics with respect to the domain. As a result, there is often a need to adapt these event types over time as the domain changes. This could involve revising an existing event type (which is fine for adding new attributes for capturing more information) or creating a new event type to model some that has changed in the domain. If you simply incorrectly modeled the events for the domain, then you will have the same challenges of migrating a poorly designed database schema.

The arguments that Git and Datomic are both event sourced systems are good examples of successful application of this pattern. However, these are poor examples when it comes to event sourcing where the events are "domain events". In both Git and Datomic, the data model of the event are pre-defined. With Git you have a changeset and with Datomic you have datoms, both of which are composable by design and where every changeset and datom is equivalent (from a structural standpoint).

Applying event sourcing to an arbitrary domain model means every event is both semantically and possibly structurally different. That is, how event of type X affects the state compared to an event of type Y is different, where as applying two different datoms or changesets in Datomic or Git, respectively, change the state in the same way.

So I think there are two fundamental challenges faced when using event sourcing with a domain model. First is that the type and structure of events need to adapt to the domain (business, organization, etc). Datoms and changesets never change.. they are fixed and therefore don't have that challenge. Second, and related, is that as new events are introduced or existing ones are adapted, etc. the code that processes those events are unique as well (not just the model of the event itself). This challenge is exacerbated if there are multiple downstream consumers of this event stream where now there is "coupling" on the event/data side of things and likely semantic coupling as well.

Again, this is not something you run into with Datomic or Git simply because the data model of the events in those systems (the fundamental unit being left-folded) has a fixed data model and semantics.

bruth··on Amazon Timestream – Fast, scalable, fully managed time series database
Really depends on the use case. Working in healthcare, vital signs can be modeled as time series points, but are lower frequency than, say, metrics from servers. However we want to store every point so a spike is not missed. One could argue an unsustained spike is noise, but in the healthcare domain there may be a correlation with some external event (the purpose is surprised and their heart rate spikes).
bruth··on Amazon Timestream – Fast, scalable, fully managed time series database
AWS re:Invent
bruth··on Ask HN: Who is hiring? (November 2018)
The Children's Hospital of Philadelphia | Arcus Data Platform Engineer | Philadelphia PA | ONSITE Please visit: https://careers.chop.edu/job/Philadelphia-RIA-Programmer-II-...

The Children’s Hospital of Philadelphia (CHOP) Research Institute is recruiting a new team to build a data and informatics program called “Arcus” that will link clinical and biological data and provide world-class computational tools to solve the most challenging problems in child health. Recognizing the central role of data to the future of pediatric research, CHOP leadership and the Board of Trustees committed to a funding plan, and Arcus was launched in July 2017. The Arcus team integrates with major scientific initiatives in the Research Institute Strategic Plan: Lifespan, Rare Diseases, Novel Devices and Therapeutics, and Precision Health. We seek mission-oriented professionals with interest and expertise in the areas of biomedical science, library science, data education, data science, cloud computing, data privacy, and security.

This role will work on a small team focused on architecting and implementing a cloud-native “data platform” to support the goals of Arcus. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

More info about CHOP and our work: http://www.chop.edu/ | https://dbhi.chop.edu/ | https://github.com/chop-dbhi

bruth··on Not Lisp again (2009)
Its a matter of time before there is a "bot" that auto-posts this kind response for historical reference.
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