User: Samuel Lampa

gravatar for Samuel Lampa
Samuel Lampa1.2k
Reputation:
1,180
Status:
Trusted
Location:
Stockholm
Website:
http://samuel.lampa.co/
Twitter:
smllmp
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Google Scholar Page
Last seen:
3 days, 22 hours ago
Joined:
7 years, 8 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 • 114 results • page 1 of 12 • next >
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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 4 days ago by Samuel Lampa1.2k
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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 16 months ago by Samuel Lampa1.2k
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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 16 months ago by Samuel Lampa1.2k
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Answer: A: Large-scale open-source bioinformatics datasets
... [Human Protein Atlas][1] [1]: http://www.proteinatlas.org/ ...
written 17 months ago by Samuel Lampa1.2k
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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 2.3 years ago by Samuel Lampa1.2k • updated 2.3 years ago by RamRS18k
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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 2.4 years ago by Samuel Lampa1.2k
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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 2.5 years ago by Samuel Lampa1.2k
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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 2.5 years ago by Samuel Lampa1.2k
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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 2.5 years ago by Samuel Lampa1.2k
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Comment: C: Is there a Lims that doesn't suck?
... Sorry, it seems it should be without HTTPS ...
written 2.5 years ago by Samuel Lampa1.2k

Latest awards to Samuel Lampa

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Epic Question 10 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?
Great Question 16 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 3.3 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Popular Question 3.3 years ago, created a question with more than 1,000 views. For List of unresolved problems in Computational Biology / Bioinformatics?
Great Question 3.6 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 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?
Centurion 3.7 years ago, created 100 posts.
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Student 3.7 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 4.0 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 4.5 years ago, created a question with more than 1,000 views. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: Picking A Programming Language And Where To Begin
Appreciated 4.6 years ago, created a post with more than 5 votes. For Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
Appreciated 4.6 years ago, created a post with more than 5 votes. For What Bioinformatics Software Is There, Written In D?
Good Question 4.6 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 4.6 years ago, asked a question that was upvoted at least 5 times. For What Bioinformatics Software Is There, Written In D?
Good Question 4.6 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 4.6 years ago, created a question with more than 1,000 views. For How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?

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