User: Samuel Lampa

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Samuel Lampa1.1k
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Location:
Stockholm
Website:
http://samuel.lampa.co/
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smllmp
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Last seen:
2 weeks ago
Joined:
6 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

<prev • 115 results • page 1 of 12 • next >
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Comment: C: Workflow management software for pipeline development in NGS
... 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 6 months ago by Samuel Lampa1.1k
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Comment: C: Workflow management software for pipeline development in NGS
... 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 6 months ago by Samuel Lampa1.1k
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Answer: A: Large-scale open-source bioinformatics datasets
... [Human Protein Atlas][1] [1]: http://www.proteinatlas.org/ ...
written 6 months ago by Samuel Lampa1.1k
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Comment: C: How to handle metadata in bioinformatics pipelines?
... 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 17 months ago by Samuel Lampa1.1k • updated 17 months ago by Ram12k
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Answer: A: What are the most popular NGS tools?
... 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 17 months ago by Samuel Lampa1.1k
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Comment: C: Benchmarking bioinformatics workflow with common patterns and motifs?
... 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 19 months ago by Samuel Lampa1.1k
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Benchmarking bioinformatics workflow with common patterns and motifs?
... 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: - ...
workflows pipelines written 19 months ago by Samuel Lampa1.1k
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Comment: C: How To Create A Bioinformatics Pipeline Using Spotify !
... Just for reference: Luigi's Monkey Wrench is nowadays deprecated in favor of [SciLuigi][1] [1]: https://github.com/pharmbio/sciluigi ...
written 19 months ago by Samuel Lampa1.1k
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Comment: C: Is there a Lims that doesn't suck?
... Sorry, it seems it should be without HTTPS ...
written 19 months ago by Samuel Lampa1.1k
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Answer: A: How To Create A Bioinformatics Pipeline Using Spotify !
... 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 2.7 years ago by Samuel Lampa1.1k

Latest awards to Samuel Lampa

Great Question 5 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?
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Popular Question 2.4 years ago, created a question with more than 1,000 views. For List of unresolved problems in Computational Biology / Bioinformatics?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Centurion 2.8 years ago, created 100 posts.
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Student 2.8 years ago, asked a question with at least 3 up-votes. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Appreciated 3.7 years ago, created a post with more than 5 votes. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Appreciated 3.7 years ago, created a post with more than 5 votes. For What Bioinformatics Software Is There, Written In D?
Good Question 3.7 years ago, asked a question that was upvoted at least 5 times. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Good Question 3.7 years ago, asked a question that was upvoted at least 5 times. For What Bioinformatics Software Is There, Written In D?
Good Question 3.7 years ago, asked a question that was upvoted at least 5 times. For Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For What Bioinformatics Software Is There, Written In D?

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