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Join the team! #27

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johanneskoester opened this Issue Nov 29, 2015 · 37 comments

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johanneskoester commented Nov 29, 2015

Everybody is welcome to officially join the team. This does not involve any duties. Just contribute features you need for your own work. To join, please post here.

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cramertj commented Feb 28, 2016

cramertj -- I'd like to help where I can. I don't have very much bio knowledge, but I'm happy to lend a hand where I can (I'm trying to get in some more Rust practice).

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johanneskoester commented Feb 29, 2016

Great, thanks! I have sent an invitation!

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Drin commented Jul 31, 2016

hello! I'd like to join the team and start working on some things. I want both practice with bioinformatics and rust, so this is a pretty good place to be, I think :)

username: drin

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johanneskoester commented Aug 1, 2016

Great to hear, welcome!

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gamazeps commented Aug 16, 2016

Hi all I'd like to help if possible, even though I'm not an expert in bioinformatic nevertheless I do have some basic knowledge of it (basically the Coursera UCSD courses on bioinformatics), I basically have the next month to kill so feel free to through features to implement on me :)

username: gamazeps

(by the way github already shows the username, why do you want it posted here ?)

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johanneskoester commented Aug 17, 2016

You are right, I changed the text ;-). Thanks for your interest in Rust-Bio!! Feel free to pick features from issue #3. Please let me know if I can help in any way. You can also propose new stuff to that list.

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bryceperkins commented Oct 6, 2016

Hey, I'm eager to help contribute features and improve my skill with rust. Let me know if there are any current project that need pushing forward.

username: bryceperkins

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johanneskoester commented Oct 18, 2016

Welcome! You can have a look at issue #3. Personally, I am currently most interested in HMM support and implementing anything from this amazing book: http://www.genome-scale.info/. But we are open to anything related to bioinformatics.

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dlaehnemann commented Oct 19, 2016

I'm new here, as well, thanks for adding me in!

I'll be using this as a way to get into Rust and will probably implement some rust-bio-tools.

Also, the book sounds quite comprehensive regarding HTS data, just ordered it. ;) Anybody interested in working through it together and implementing some data structures and algorithms along the way?

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johanneskoester commented Oct 19, 2016

Glad to hear that. Indeed, Veli's book is an excellent read. If I had the time, I would go through it myself. Unfortunately I can't at the moment. But anything from it would be a perfect fit for Rust-Bio. Thinking about the current trends, the graph genome stuff would be most interesting of course.

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Drin commented Oct 19, 2016

I would be interested in a regular web meeting of some sort. I have the
book, but will be in Korea for another 3 and a half weeks.

On Oct 19, 2016 23:31, "Johannes Köster" notifications@github.com wrote:

Glad to hear that. Indeed, Veli's book is an excellent read. If I had the
time, I would go through it myself. Unfortunately I can't at the moment.
But anything from it would be a perfect fit for Rust-Bio. Thinking about
the current trends, the graph genome stuff would be most interesting of
course.


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dlaehnemann commented Oct 20, 2016

Cool, just let me know once you're back and ready to go. And once we decide on a web meeting / exchange format, we can post it here for further interested people to join.

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Drin commented Nov 15, 2016

@dlaehnemann I'm back home now, ready to go whenever!

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dlaehnemann commented Nov 16, 2016

@Drin Good to hear. Currently, I'm still waiting for my copy of the book -- it seems to have gotten lost on the way and I'll have to wait for another shipping. But I have gone ahead and created an Etherpad where we can coordinate our study group, thus other people who are interested can just head there and join in:
http://pad.learninglab.de/p/GSAD

Please feel free to extend that document, e.g. by adding more of the chapter structure. I'll try and join in as soon as possible, but might only have considerable amounts of time to invest in some time in March / April...

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Drin commented Nov 16, 2016

We can go at whatever pace is reasonable for us. I'm in no rush, and have
plenty of other things competing for attention :)

On Nov 16, 2016 05:56, "David Laehnemann" notifications@github.com wrote:

@Drin https://github.com/Drin Good to hear. Currently, I'm still
waiting for my copy of the book -- it seems to have gotten lost on the way
and I'll have to wait for another shipping. But I have gone ahead and
created an Etherpad where we can coordinate our study group, thus other
people who are interested can just head there and join in:
http://pad.learninglab.de/p/GSAD

Please feel free to extend that document, e.g. by adding more of the
chapter structure. I'll try and join in as soon as possible, but might only
have considerable amounts of time to invest in some time in March / April...


You are receiving this because you were mentioned.
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bpr commented Nov 25, 2016

I've been investigating kmer counting (over DNA nucleotides) and since I didn't notice anything in rust-bio I hacked up a kmer iterator over TextSlice and quickly wrote a naive counter. I'd be happy to give the code to rust-bio and work with others to get some Jellyfish-like parallel counter with lock free hash tables and the like.

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johanneskoester commented Nov 25, 2016

Hi @bpr. Glad to hear that! Feel free to submit a PR!

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klangner commented Mar 4, 2017

Hi,
I would like to learn Rust by contributing to this project. I hope to get some tips during the code review :-)

But since I don't work in bioinformatics domain, may I ask if anybody is using this library for any work in this domain? If yes could you share which functionality and what is missing?

I saw that #3 contains list of requested features. Is it up to date? It was edited almost 2 years ago if I'm not mistaken? I was wandering what could be an easy task for beginners like me :-)

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johanneskoester commented Mar 6, 2017

Welcome @klangner! We are looking forward to your contributions. From the download numbers Rust-Bio is used for various projects, but it is hard to keep track, especially since many of them are presumably still unpublished. Of course, I know about my own stuff, which currently uses fmindex and stats. Then, there is @pmarks, who uses at least alignment with his company. The feature list is still up to date. A fairly general topic that needs no bio knowledge would be support for hidden markov models (viterby algorithm, baum-welch and so on). Issue #3 has been updated in the meantime, but it seems like github is not changing the modification date when you just check one of the bullets.

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klangner commented Mar 6, 2017

Thanks,

I'm interested in HMM. I need this for my own work, which is related to sensors and hydrology.
And since this this library will be used for our company internal projects I would prefer to make it as separate more general library outside of rust-bio. I don't want to explain, to other people in my company, why we need bio library to filter precipitation time series ;-)
But If you will be interested in adding external HMM lib to the rust-bio, then I can make necessary bindings here and add the features which are needed in rust-bio.

What do you think about this?

For our case I will need both inference and learning. Is learning HMM also important in bio? Or the models are roughly known?

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johanneskoester commented Mar 6, 2017

I am perfectly fine with a separate crate for HMMs. Once you have a repo, please let me know and I'll watch the progress. Once the basic functionality is there, we can see whether rust-bio needs integration or whether it should just be used as a separate crate. I think all kinds of HMM functionality is of importance in bioinformatics. But indeed, the most common use case is that the model is known.

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klangner commented Mar 6, 2017

Great :-)

I have created git repo for this project:
https://github.com/klangner/hmm

I will work there.

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johanneskoester commented Mar 6, 2017

Great, I am really looking forward to this!

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m1guelpf commented Mar 23, 2017

Hi!

I've created a tool called OrgManager that allows you to generate links to join a Github organization!
(You may want to get more info at the github repo or see it in action.)

Some organizations like Open Source Design are using it to make joining faster!

It even has an API, if you want to integrate it with your application!
(Api docs)

What do you think?

PD. If you think it could have other nice features, just open an issue on the repo!

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RHagenson commented Jun 4, 2017

Thought I should do a quick introduction of myself somewhere and here seemed the best place.

Name and education

The name is Ryan Hagenson and I will be defending my master's thesis in Biomedical Informatics in a little over one month. I currently hold a BS in Biochemistry and Molecular Biology where I did bioinformatics work with Perl, but mostly worked as a lab technician. For my Master's, I studied the relationship between protein disorder and cancer subtypes leveraging TCGA data. In this work I used R and Python which were sufficient, but nearing the end of my education I focused on scaling bioinformatics work since our datasets are only getting larger and more unwieldy. I happened across Rust and this team in the process.

Contribution plans

However, I recently began work as a Bioinformatics Technician where I will primarily be doing phylogenetics studies so that is where I plan to expand Rust-Bio's capabilities as I build in-house tools. However, between continuing to use my lab's previous methods outside of Rust and finalizing my MS thesis, I imagine my contributions will be pretty basic for the first few months (like adding the RNA alphabet which was missing, reviewing the docs to have a consistent voice/word choice, adding tests to increase coverage or provide edge case examples, etc.).

Criticisms more than welcome

As I contribute, I wish to invite criticisms to my work -- especially as my contributions become more substantial. What makes sense to me might be a poor design choice when looked at by someone else so feel free to let me know when you see a problem.

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johanneskoester commented Jun 5, 2017

Great, I am glad to have you joining the team @RHagenson! I am looking forward to your contributions!

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bnbowman commented Dec 31, 2017

Hi, I'd like to join the team, to add some support for algorithms and tools for various long-read technologies (e.g. PacBio, Oxford Nanopore)

My name is Brett - I have a Master's in Bioinformatics and currently work for Pacific Biosciences developing new tools for medical diagnostics. In fact I used I used to work with @pmarks before he left to join the Dark-side - anything I can claim to know about functional programming I can lay at his feet for the giant pile of F# code he left me with ;-P .

My motivations are as follows:
(1) To develop my own software engineering skills and Rust-language skills in particular
(2) To deepen my understanding of core bioinformatics algorithms, particularly those useful for working with long-read technologies
(3) To provide support for other scientists interested in working with long-read sequencing data in Rust

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nunesdaniel commented Jan 2, 2018

Hi, I would like to join and Contribute to it.

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johanneskoester commented Jan 3, 2018

Hey @bnbowman and @nunesdaniel I am glad to welcome you in the team! @bnbowman I am also excited to see that a second company after 10x becomes interested in Rust-Bio! I am looking forward to work with the two of you!

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wizofe commented May 12, 2018

Hi, there! Currently pursuing a MSc. in Bioinformatics and I was also selected for the summer of code in Redox OS. Very happy to add something if I can ^_^

@wizofe wizofe referenced this issue May 13, 2018

Open

Roadmap / Todos #3

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brianjimenez commented Aug 16, 2018

Hi there! PhD in bioinformatics, mainly in structural biology, but with a strong background in research software engineering. I'd like to contribute to this wonderful initiative as I'm learning Rust and I know a little bit of structures and PDB format.

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johanneskoester commented Sep 5, 2018

Hi @brianjimenez and @wizofe! Sorry for the late reply, I have been on vacation. You should have invitations now.

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k3yavi commented Nov 30, 2018

Hey guys, was just browsing over the issues for using rust-bio with nightly and stumble upon this thread and just wanted to say Hi! I am a PhD student in Computer Science and have mainly worked before in C++ and python. I'd love to contribute but usually would be based on the requirement of the projects and the boss ;p.
Currently working with @rob-p and have gained some rust experience while interning at 10x (w/ @pmarks) to create and extend read-mapper, debruijn graph, Minimum perfect hash rust libraries.

PS: pointers for using rustbio with nightly is appreciated ;p

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johanneskoester commented Dec 1, 2018

Welcome @k3yavi! Any kind of contribution is much appreciated! Glad to see Rust in bioinformatics getting more and more users. Greetings to Rob! We do not test systematically on nightly, but usually it is not more than a few adjustments away to get it to work. Feel free to file an issue, and I see how I can help.

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k3yavi commented Dec 2, 2018

Thanks @johanneskoester , glad to be a part of the team. re: issues -- will do .

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kanishka-azimi commented Dec 21, 2018

I have a lot of free time in December and early January if anybody here wants to join me in running a short hack night in the greater NYC area for rust-bio. People can email me at nish2575 at gmail, if they want to attend or help coordinate.

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johanneskoester commented Jan 3, 2019

Welcome @kanishka-azimi!

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