User: Samuel Lampa
Samuel Lampa • 1.2k
- Reputation:
- 1,180
- Status:
- Trusted
- Location:
- Stockholm
- Website:
- http://samuel.lampa.co/
- Twitter:
- smllmp
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- Last seen:
- 1 month, 4 weeks ago
- Joined:
- 7 years, 9 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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Answer:
A: On the usage of Golang
... I have mostly written workflow software in Go (SciPipe), not that much low-level algorithmic stuff. Based on my experiences though, if I'd go into algorithmic development, I'd:
1. Choose Go if I'd aim to create a library of components or functions, where I want to use the same language both for the ...
written 9 weeks ago by
Samuel Lampa • 1.2k
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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 18 months ago by
Samuel Lampa • 1.2k
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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 18 months ago by
Samuel Lampa • 1.2k
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... [Human Protein Atlas][1]
[1]: http://www.proteinatlas.org/ ...
written 19 months ago by
Samuel Lampa • 1.2k
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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 2.5 years ago by
Samuel Lampa • 1.2k
• updated
2.5 years ago by
RamRS ♦ 19k
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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 2.5 years ago by
Samuel Lampa • 1.2k
0
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853
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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 2.6 years ago by
Samuel Lampa • 1.2k
3
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853
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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 2.6 years ago by
Samuel Lampa • 1.2k
0
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3
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3
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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 2.6 years ago by
Samuel Lampa • 1.2k
0
votes
20
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31k
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20
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... Sorry, it seems it should be without HTTPS ...
written 2.6 years ago by
Samuel Lampa • 1.2k
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For A: Picking A Programming Language And Where To Begin
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12 months ago,
created a question with more than 10,000 views.
For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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18 months ago,
created a question with more than 5,000 views.
For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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created a question with more than 1,000 views.
For Luigi's Monkey Wrench - A small helper library for commandline heavy bioinformatics workflows in Spotify's Luigi workflow tool
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3.5 years ago,
created a post with more than 5 votes.
For A: Picking A Programming Language And Where To Begin
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created a question with more than 1,000 views.
For What Academic Hpc (Or Cloud) Infrastructures For Ngs Data Analysis And Storage Are There?
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created a question with more than 1,000 views.
For Hints For Integrating The Integrative Genomics Viewer (Igv) In Other Java Based Software?
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created a question with more than 1,000 views.
For List of unresolved problems in Computational Biology / Bioinformatics?
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3.7 years ago,
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For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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3.9 years ago,
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For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
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For A: Picking A Programming Language And Where To Begin
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3.9 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 A: Picking A Programming Language And Where To Begin
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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 What Bioinformatics Software Is There, Written In D?
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For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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4.7 years ago,
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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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For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
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For How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?
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