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Ask HN: What is your job role and what are the side projects you are working on?

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Re: Ask HN: What is your job role and what are the side projects you are working on?

#51

Post by adenadel »

rfc wrote: post #19
aryamaan wrote: post #12

Earlier quoted context omitted.

Sounds interesting.

Thanks. We're pretty excited about it. There's lots of big challenges to solve, especially on the data from. Full 30x coverage of a human genome is (uncompressed) around 180gb. So the core problem we're trying to solve right now is: 1) Compressing the files locally and sending via FTP to server 2) Aligning 180gb files against the reference genome (180gb also) in less than 5 minutes 3) Storing that data in a performan…

Is anyone using your pipeline? There are lots of fully developed commercial pipelines for human WGS (Illumina BaseSpace, DNAnexus, Seven Bridges, etc.) Depending on the hardware you have available bowtie2 might not be the best aligner. What are you using for variant calling? If you're using the GATK Haplotype caller you're going to have issues with commercial licensing.

Re: Ask HN: What is your job role and what are the side projects you are working on?

#52

Post by atmosx »

My day-job role is pharmacist. Although 'Pharmacy Manager' is a more accurate[1] description of what I do. I also work as remote sys-admin for a couple of US-based startups. Add to that I'm studying for my final MDPharm exam(!).

My side-projects are argosnap[2] and on a RoR application which came out of the need for an application to manage/keep track of customers credit and I'm planning to make a SaaS out of it.

[1] I micro and macro-manage our family pharmacy. I also work on the bench. I have 5+ years of managerial experience in the secondary sector (~ 150 ppl business) and I assure you that the amount of managerial work required by a medium-sized pharmacy in Greece is astonishing.

[2] http://www.convalesco.org/argosnap/ - a tarsnap notification utility.

Re: Ask HN: What is your job role and what are the side projects you are working on?

#53

Post by haidrali »

My Job is "Full Stack Web Developer" at Void Labs and In my side project I am currently doing PollPK.com, A website which let user publish polls and other user can vote on those polls ( just like Reddit user can post links and other can comment ) Here is my early beta http://beta.pollpk.com/ example polls would be like anything e.g. Who is the top football in the world ( Ronaldo, Messi etc ) Who is the current best actor ( Johnny Depp, Leonardo DiCaprio etc )

Re: Ask HN: What is your job role and what are the side projects you are working on?

#55

Post by aryamaan »

JoeAltmaier wrote: post #35

I'm an OS/embedded programmer contracting to companies across the USA. Currently porting android to a panel controller for some industrial equipment (I honestly don't know what; it hardly matters). My side projects are gaming-related.

You develop games?

Re: Ask HN: What is your job role and what are the side projects you are working on?

#56

Post by orless »

On may day job, I'm a senior software architect for the Deutsche Bahn (German Railways).

On my free time, I work on a number of open-source projects (see https://github.com/highsource). For instance:

* https://github.com/highsource/maven-jaxb2-plugin - probably the most advanced Maven plugin for JAXB

* https://github.com/highsource/jsonix - Powerful XMLJS mapping library in pure JS

* https://github.com/highsource/jsonix-schema-compiler - XML Schema->Jsonix mappings compiler, also XML Schema->JSON Schema converter

* https://github.com/highsource/jaxb2-basics - a set of plugin for JAXB (like equals/hashCode/toString generation and more)

* https://github.com/highsource/ogc-schemas - compiled GIS XML Schemas

And a few more.

Re: Ask HN: What is your job role and what are the side projects you are working on?

#57

Post by rfc »

adenadel wrote: post #51
rfc wrote: post #19

Earlier quoted context omitted.

Thanks. We're pretty excited about it. There's lots of big challenges to solve, especially on the data from. Full 30x coverage of a human genome is (uncompressed) around 180gb. So the core problem we're trying to solve right now is: 1) Compressing the files locally and sending via FTP to server 2) Aligning 180gb files against the reference genome (180gb also) in less than 5 minutes 3) Storing that data in a performan…

Is anyone using your pipeline? There are lots of fully developed commercial pipelines for human WGS (Illumina BaseSpace, DNAnexus, Seven Bridges, etc.) Depending on the hardware you have available bowtie2 might not be the best aligner. What are you using for variant calling? If you're using the GATK Haplotype caller you're going to have issues with commercial licensing.

No one is using it yet. Still just a side project :)

Seven Bridge & DNAnexus probably have the most complete/thorough system (imo). The challenge though is doing it fast, at scale, and user friendly enough. Seven Bridges is cost effective and can definitely scale but it's not necessarily the fastest solution on the market. While these guys offer the full end-to-end solution, we're just trying to focus specifically on accelerating the pipeline. Maybe in the future we'll get to the full circle, but that's not our focus.

We use a variation of bowtie2 that allows us to scale well. We're able to align a 30x genome right now in about 8 minutes and are doing a couple more tests that might get us down into the There are universities, such as Harvard, that are trying to align 1,000s of these a month but the current providers can't keep up. So, we're seeing if we can provide something that can help them out.

Re: Ask HN: What is your job role and what are the side projects you are working on?

#58

Post by sheraz »

CTO by day (apps and search)

http://helloaviva.com - By night I work on a niche app for city-parents to find changing tables, nursing rooms, and play areas

http://www.3cosystem.com - where I map out all the tech and startup events for 60+ cities world-wide

Re: Ask HN: What is your job role and what are the side projects you are working on?

#59

Post by adenadel »

rfc wrote: post #57
adenadel wrote: post #51

Earlier quoted context omitted.

Is anyone using your pipeline? There are lots of fully developed commercial pipelines for human WGS (Illumina BaseSpace, DNAnexus, Seven Bridges, etc.) Depending on the hardware you have available bowtie2 might not be the best aligner. What are you using for variant calling? If you're using the GATK Haplotype caller you're going to have issues with commercial licensing.

No one is using it yet. Still just a side project :) Seven Bridge & DNAnexus probably have the most complete/thorough system (imo). The challenge though is doing it fast, at scale, and user friendly enough. Seven Bridges is cost effective and can definitely scale but it's not necessarily the fastest solution on the market. While these guys offer the full end-to-end solution, we're just trying to focus specifically on…

Don't worry, I work for a company in the space and fully understand the challenges :) I have a really hard time believing that you can align a 30x genome in 8 minutes because the I/O time is longer than that, and bowtie doesn't use one of the faster algorithms for alignment (usually the kmer hashing methods are faster when you have machines with enough memory. Microsoft's snap and Illumina's isaac are two examples). What kind of hardware are you benchmarking on?

Re: Ask HN: What is your job role and what are the side projects you are working on?

#60

Post by rfc »

adenadel wrote: post #59
rfc wrote: post #57

Earlier quoted context omitted.

No one is using it yet. Still just a side project :) Seven Bridge & DNAnexus probably have the most complete/thorough system (imo). The challenge though is doing it fast, at scale, and user friendly enough. Seven Bridges is cost effective and can definitely scale but it's not necessarily the fastest solution on the market. While these guys offer the full end-to-end solution, we're just trying to focus specifically on…

Don't worry, I work for a company in the space and fully understand the challenges :) I have a really hard time believing that you can align a 30x genome in 8 minutes because the I/O time is longer than that, and bowtie doesn't use one of the faster algorithms for alignment (usually the kmer hashing methods are faster when you have machines with enough memory. Microsoft's snap and Illumina's isaac are two examples).…

Check out NVBowtie. We don't use standard CPUs to do the alignment. The benchmarks were ran on 2 Nvidia K80s which were in the same blade. To scale it, you need Infiniband between the blades (found this out the hard way). The genomes are loaded into memory to reduce read times.

Just to be clear, we're not reading this directly off of the sequencers. Our assumption is the sequenced data is already stored in which we load the data onto the cluster.

I'm not necessarily the technical one of our group unfortunately but, if you're interested, I'd be interested in picking your brain.

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