User: me

gravatar for me
me610
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610
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Location:
Switzerland
Twitter:
@jervenbolleman
Last seen:
12 hours ago
Joined:
3 years, 9 months ago
Email:
m*@jerven.eu

Posts by me

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Substring dereplication of protein sequences
... [pir peptide search][1] could be helpful even if it does not answer your question. [1]: https://research.bioinformatics.udel.edu/peptidematch/commandlinetool.jsp ...
written 6 weeks ago by me610
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Comment: C: UniProt ID mapping API call
... Well they would be in a significant part be me ;) You can use the upload list facility on www.uniprot.org as well. Then you can use what ever columns you want. The real difficulty is actually with gene names and how they map to/from UniProt entries. The solutions to that are ask for exactly what you ...
written 8 weeks ago by me610
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Comment: C: UniProt ID mapping API call
... if you want the species/ncbi taxid just add a line "?protein up:organism ?taxon ." at the end of the where clause and "?taxon" on the select line. ...
written 8 weeks ago by me610
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Answer: A: UniProt ID mapping API call
... You can use requests like http://www.uniprot.org/uniprot/?query=accession:P13368&format=tab&columns=genes to access only the gene names. However, the delimiting is a bit odd to parse in this case. i.e. some entries are linked to more than one gene. And genes often have more than one na ...
written 8 weeks ago by me610
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Comment: C: Fortran 95 script that converts .xyz files into pdb files
... You might want to explain why you need it in exactly fortran95 and nothing else will do. ...
written 12 weeks ago by me610
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Answer: A: What's fascinating about Bioinformatics for potential students?
... What I enjoy now 10 years into the field is that I get to do quite cutting edge computer science but always to solve a real problem that helps biologists. This mix of using theory to advance practical solutions is just wonderful. A second benefit is that people who solve problems using computers are ...
written 12 weeks ago by me610
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Comment: C: Fortran 95 script that converts .xyz files into pdb files
... You can do the conversion with [openbabel][1] but that is not written in fortran 95. [1]: http://openbabel.org/wiki/Main_Page ...
written 12 weeks ago by me610
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Comment: C: Describe Your Architecture: Uniprot (2017)
... Don't follow the UniProt architecture it is too niche and not appropriate for you at this point in time. It's a formula 1 car and I am not sure that you are the stage where you need a moped or can still bike ;) Jena TDB, Virtuoso will scale to a few 100 million of sequences given a reasonable hardw ...
written 3 months ago by me610
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Answer: A: Describe Your Architecture: Uniprot (2017)
... **Recommendation for a new site project** Just put it in RDF and pick any SPARQL store. Mostly, if you don't know what your usage is going to be like it's much better to be very flexible in the way you can retrieve data eating some cost in CPU/hardware inefficiency to get more of that flexibility. ...
written 3 months ago by me610
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Answer: A: Describe Your Architecture: Uniprot (2017)
... This is an update to the answer [here][1] considering the architecture of the UniProt website. This is an architecture that makes sense for us but is not something I would recommend to anyone generally without really thinking hard about it. **UniProt website architecture in 2017** UniProt is a con ...
written 3 months ago by me610

Latest awards to me

Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Downloading dataset of PTM sites from UniProt
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar 8 weeks ago, created an answer that has been accepted. For A: Does UniProt have complete SNP information (from dbSNP)?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar 14 months ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Supporter 14 months ago, voted at least 25 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Scholar 3.2 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Scholar 3.3 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Scholar 3.4 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R

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