User: Samuel Lampa
Samuel Lampa • 1.1k
- Reputation:
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- Location:
- Stockholm
- Website:
- http://samuel.lampa.co/
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- smllmp
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- Last seen:
- 6 months, 2 weeks ago
- Joined:
- 7 years, 4 months ago
- Email:
- s***********@bils.se
Developer at Bioinformatics Infrastructure for Life Sciences (BILS) in Stockholm and PhD student at Dept of Pharmaceutical Biosciences at Uppsala University, developing and researching on the topic of handling large-scale data and computations on HPC clusters.
Posts by Samuel Lampa
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... For proper reference I need to mention that our experience resulted in the SciLuigi helper library on top of luigi:
https://github.com/pharmbio/sciluigi (Though nowadays we are taking the ideas even further with http://scipipe.org). ...
written 13 months ago by
Samuel Lampa • 1.1k
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... Nice points! I think your number 2. bonus point is what use to be referred to as "sub-workflow" support, or sometimes "sub-network" support.
I really like point #1 and bonus point #1 too ... they make me think ... :) ...
written 13 months ago by
Samuel Lampa • 1.1k
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... [Human Protein Atlas][1]
[1]: http://www.proteinatlas.org/ ...
written 13 months ago by
Samuel Lampa • 1.1k
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... I'm not sure I understand exactly what you mean with metadata. Could you clarify that a little? Do you mean a description of the outputs you want the workflow to produce?
Part of your description sounds like something I've been ranting [before][1], about the need for dynamic workflow scheduling, wh ...
written 2.0 years ago by
Samuel Lampa • 1.1k
• updated
2.0 years ago by
Ram ♦ 15k
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... We tried to create an approximate [such list][1] at one HPC center mainly running NGS workloads, based on "module" loads (via the GNU module system), which indicates everytime a script is loading a module for an installed software on the system (it had lots).
[The list][1] is from a few years ago ( ...
written 2.0 years ago by
Samuel Lampa • 1.1k
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... Indeed. I'm looking for something as realistic as possible, and simple concrete examples would be optimal.
I just want to make sure that most relevant patterns, or "type examples" are covered. E.g. the above examples are some motifs that we have came across in our own work with applying machine lea ...
written 2.2 years ago by
Samuel Lampa • 1.1k
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... Is anyone aware of a good example workflow that incorporates some of the most common workflow motifs or patters, in bioinformatics workflows, that could be used to try out various workflow engines and see how easy it is to encode the workflow in them?
Some examples of what I mean with patterns:
- ...
written 2.2 years ago by
Samuel Lampa • 1.1k
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... Just for reference: Luigi's Monkey Wrench is nowadays deprecated in favor of [SciLuigi][1]
[1]: https://github.com/pharmbio/sciluigi ...
written 2.2 years ago by
Samuel Lampa • 1.1k
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20
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... Sorry, it seems it should be without HTTPS ...
written 2.2 years ago by
Samuel Lampa • 1.1k
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... For some bioinformatics tasks, the extra boilerplate needed with luigi can be a bit hampering. This lead me to write a little (~50 lines of code) helper library that lets you define inputs and outputs inline in the command pattern, and connect inputs and outputs between tasks using single-assignment ...
written 3.3 years ago by
Samuel Lampa • 1.1k
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For Luigi's Monkey Wrench - A small helper library for commandline heavy bioinformatics workflows in Spotify's Luigi workflow tool
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For A: Picking A Programming Language And Where To Begin
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For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
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For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
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4.2 years ago,
asked a question that was upvoted at least 5 times.
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Good Question
4.2 years ago,
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For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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4.2 years ago,
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For How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?
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For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
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For What Bioinformatics Software Is There, Written In D?
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