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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?

#61

Post by adenadel »

rfc wrote: post #60
adenadel wrote: post #59

Earlier quoted context omitted.

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 l…

Ah, gpus are cheating... :) What I meant about i/o is that if you're reading the data off of disc your read/write time is probably longer than 8 minutes. With SSDs you can obviously go faster. One problem with scaling is that you need a bunch of machines that have the gpus available (although if you can get the whole pipeline under 30min you wouldn't need many machines). The cloud genomics companies mostly use AWS and Google cloud for their compute and I don't know what sorts of non CPU compute resources are available. You would probably be interested in looking into Edico Genomics' Dragen FPGA. Is there a way to PM on HN?

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

#62

Post by rfc »

adenadel wrote: post #61
rfc wrote: post #60

Earlier quoted context omitted.

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 l…

Ah, gpus are cheating... :) What I meant about i/o is that if you're reading the data off of disc your read/write time is probably longer than 8 minutes. With SSDs you can obviously go faster. One problem with scaling is that you need a bunch of machines that have the gpus available (although if you can get the whole pipeline under 30min you wouldn't need many machines). The cloud genomics companies mostly use AWS an…

Get in touch with me here: http://bit.ly/1OX84Nb

Would love to talk more :)

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

#63

Post by Veratyr »

I'm a software engineer working on internal business tools.

My current side project is evaluating academically published demosaic algorithms for camera sensors by implementing them with Halide (halide-lang.org) and running them against my personal photos.

I'm mainly aiming to learn about how camera sensors actually work and what the image processing pipeline looks like between a bunch of RGGB pixels and a JPEG. I'm hoping to build my own pipeline but I may also contribute my implementations to RawTherapee, if the papers' authors permit.

Learning Halide is also fun. It's amazing how fast a computer runs when you use optimised code.

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

#64

Post by rubicon33 »

-- Day Job--

Senior Software Engineer (currently iOS).

-- Side Project --

I'm building a web betting platform, for E-Sports! My goal is to provide THE BEST option, available internationally, for betting on E-Sport games. It's a really exciting project that I've been working on for 2 years. I'm using AngularJS, and WebSockets to create a 'real-time' user experience on the client side.

-- Shameless Plug --

If you're interested in Co-Founding, I'm interested in talking to you.

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

#65

Post by noname123 »

rfc wrote: post #48
noname123 wrote: post #34

Earlier quoted context omitted.

Out of curiosity, what genome assembler are you using for your project? (I'm having to build a genome assembly pipeline with a reference assembly as well for a bioinformatics class I'm auditing at a local college, not a professional in this field either). The papers I am reading and trying to replicate uses SMALT.

Assuming you're referring to the alignment side of things. We use a variation the Bowtie2 algorithm that allows us to align multiple genomes at once to the same reference genome.

Thanks for your reply, rfc. In my Bioinformatics class, we went through Bowtie algorithm funny enough last week (the vague details I still remember are the funny way it compresses fragments as rotations and then goes onto transform the rotations). Gl on your project.

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

#66

Post by rohitksh »

My day job is of a full stack developer

Side Projects:

jquery-fade-slider - http://jqueryfadeslider.com

A jQuery plugin to add fade effect to your slider items

Google Drive Browser - http://rohit-sharma.in/Google-Drive-Browser

A mini-app which lets you get the list of files from your drive which are modified most recently

Places App - http://places.rohit-sharma.in

A foursquare like application

isbndbjs - http://rohit-sharma.in/isbndbjs

An SDK for retrieving data from ISBNDB

http-requestor - http://rohit-sharma.in/http-requestor

A Wrapper around Net/HTTP which allows you to perform HTTP Requests

rails-gsa - http://rohit-sharma.in/rails-gsa

Integrate GSA(Google Search Appliance) with your rails application

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

#67

Post by nicbou »

Current job: front end developer for a well-known mapping product (no, not that one), although my contract ends in a month.

Side projects: http://markdownnotes.com, and many, many others. I also write picture-rich articles about history: http://en.nicolasbouliane.com/blog/the-berlin-airlift

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

#68

Post by krn320 »

I’m a game programmer working on mobile games for iOS and Android, using mostly Unity game engine.

As a side project I’m also making a game (how surprising!), but I can’t share any details in case someone steals the idea and makes even better game out of it ;)

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

#69

Post by adam-_- »

My day job is a backend developer for a job startup.

For the past few years I've been on and off working on a side project to create meetup for cyclists: http://cowbellhq.com.

A few years is too long but I find it very hard to focus dedicated time to the project outside of work, friends and hobbies.

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