User: Liam Thompson

gravatar for Liam Thompson
Liam Thompson110
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110
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Location:
Gothenburg, Sweden
Last seen:
3 months, 1 week ago
Joined:
7 years, 10 months ago
Email:
d******@gmail.com

Posts by Liam Thompson

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How to Demultiplex dual indexed Illumina reads
... You can check out a beta python script on a repo at [Github][1]. I had a similar problem a few years back, and used it. Let me know if it sorts out your problem. [1]: https://github.com/dejmail/Udekwu-Bioinformatics ...
written 3 months ago by Liam Thompson110
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Answer: A: Dn/Ds Ratio - Paml : How Is It Possible To Obtain Negative Values For Dn Or Ds ?
... From my understanding of the output of the program, which is limited, an infinity values means means that there are one or more non-synonymous substitutions and no synonymous substitutions in the branch. Obviously an infinity value makes the data difficult to analyse and thus an LRT should ideally b ...
written 5.5 years ago by Liam Thompson110
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Comment: C: How To Parallelize Codeml With Python
... Yes, a python or shell script wrapper would be useful in this instance. I hope that either these jobs are small or you're running these multiple instances on a cluster/GRID system. ...
written 5.9 years ago by Liam Thompson110
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Answer: A: How To Parallelize Codeml With Python
... I do not know of any way to have parallel PAML computations on one dataset. I spent a fair amount of time looking into this and was assured by computational experts that I would need to reprogram the C(?) based PAML to allow for multi-processor or parallel computation support. I don't think this is ...
written 6.0 years ago by Liam Thompson110
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Comment: C: Apply For Supercomputing Time
... @ Flow - you would generally find out using the interface how many core hours you can get, this can be automated in the submission script and you find out within 5 minutes. I only have experience with the SAGrid, and the time between application and award was never more than 5 minutes. ...
written 6.0 years ago by Liam Thompson110
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Comment: C: Apply For Supercomputing Time
... @Pablo - We'll agree to disagree about the definition :-), although I agree that the usability of AWS is perhaps easier. The nice thing about the GRID, especially if you have very large datasets, is that you DO NOT pay for it. Each organisation agrees to contribute what resources it has. There are m ...
written 6.0 years ago by Liam Thompson110
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Comment: C: Apply For Supercomputing Time
... Cloud and Grid are essentially the same thing. For grid services however, you don't generally pay for the extra available hardware which I suspect you would pay for on a cloud machine as the institutes sign MOAs which allow the sharing of resources. ...
written 6.6 years ago by Liam Thompson110
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Answer: A: Apply For Supercomputing Time
... It looks like the Dutch Grid is connected to the other clusters on the grid. All you really need to do is follow the wiki's which most of the sites will have. Initially you would need to become part of a Virtual Organisation (VO), in my case, SAGrid, you would have to check with your local instituti ...
written 6.6 years ago by Liam Thompson110
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Answer: A: Apply For Supercomputing Time
... You could apply to become a user of the GRID. In SA we make use of the resources made available by http://roc.africa-grid.org/. It is the same as cloud computing although people would argue with me about this. Essentially, all the collaborating institutions combine their cluster computing resources ...
written 6.6 years ago by Liam Thompson110
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Answer: A: Multiple Sequence Alignment Of Thousands Of Proteins
... Have you tried MUSCLE ? I've only used it for hundreds of sequences, and it produced a good alignment in good time. I think with a cluster or a beefy desktop it would probably work nicely. ...
written 6.7 years ago by Liam Thompson110

Latest awards to Liam Thompson

Popular Question 15 months ago, created a question with more than 1,000 views. For Alignment Of Split Orfs
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Multiple Sequence Alignment Of Thousands Of Proteins

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