User: paulparsons

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paulparsons130
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130
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Location:
Canada/London/Western
Website:
http://www.csd.uwo.ca/...
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Google Scholar Page
Last seen:
3 years, 3 months ago
Joined:
5 years, 4 months ago
Email:
p**********@gmail.com

Research Scientist at IBM Canada and Postdoctoral Fellow at Western University

Posts by paulparsons

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Code for interactive web-based chromosome ideogram viewer?
... Update: The code that I posted above is being hosted here now, in the new biojs registry. For a number of reasons, it is not suitable for the project that I'm working on. A student that I'm supervising has rewritten the code to add some functionality and use vector graphics (d3.js). You can see the ...
written 4.1 years ago by paulparsons130
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Comment: C: Programmatically convert cytoband location to genomic coordinates
... This works well wrapped in a PHP script. Now I have a service on my server that I can pass any cytoband to and get back the coordinates. Thanks. ...
written 4.2 years ago by paulparsons130
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Programmatically convert cytoband location to genomic coordinates
... Is there any way to convert a cytoband location (e.g., 17p13.3) to its genomic coordinates programmatically (i.e., without having to do a manual conversion)? A web API such as BioMart would be ideal, but I haven't found a way to do it this way. Entrez Eutils would also be okay, but I likewise haven' ...
api cytoband written 4.2 years ago by paulparsons130 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: Code for interactive web-based chromosome ideogram viewer?
... Excellent. That looks like a viable option. I downloaded and played with Circos a bit, but will have to investigate it more throughly. The solution that I posted is much easier to get up and running. This is probably still a great option if one wants a circular ideogram. ...
written 4.6 years ago by paulparsons130
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Answer: A: Code for interactive web-based chromosome ideogram viewer?
... I just came across this, and got it up and running quite easily: https://www.ebi.ac.uk/Tools/biojs/registry/Biojs.Chromosome.html Pretty  much exactly what I was looking for in my original question. ...
written 4.6 years ago by paulparsons130
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Code for interactive web-based chromosome ideogram viewer?
... Does anyone know if there is any available code for an interactive web-based ideogram viewer? It would likely be written in javascript. I want to show an ideogram that dynamically displays some annotations (genes related to a phenotype search, for example).  I have found this ideogram viewer, but i ...
open source ideogram javascript written 4.6 years ago by paulparsons130 • updated 2.4 years ago by DCGenomics310
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Comment: C: Index MEDLINE/PubMed with Apache Solr
... Thanks for the comment. I wasn't necessarily making any assumptions about the difficulty of indexing . I do appreciate (at least to some degree) the challenge of indexing the journal citations.  I have previously parsed the xml citations and loaded them into a relational database. However, I've rec ...
written 4.9 years ago by paulparsons130
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Index MEDLINE/PubMed with Apache Solr
... I am interested in doing some natural language processing on the corpus of MEDLINE/PubMed journal citations. I have recently become aware of Apache Solr, which is a Lucene-based search server. I have no experience with Solr, but from what I can tell it seems to be a good way to go about tackling my ...
pubmed solr lucene medline nlp written 4.9 years ago by paulparsons130 • updated 22 months ago by Maria_Levchenko60
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Answer: A: Difference between NCBI Entrez formats (e.g., xml, docsum) for efetch
... Turns out that with EDirect, efetch -format docsum is the same as the e-utils summary, whereas efetch -format xml is the same as e-utils efetch. Here's an answer I received from NCBI: The edirect efetch is wrapper to a combination of two eutils fcgis; efetch.fcgi and esummary.fcgi. Basically the ...
written 4.9 years ago by paulparsons130
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Comment: C: Specify Assembly for NCBI Entrez Query
... Good point. In my case (although maybe not in all cases), the difference doesn't really matter, and I can get the information that I need. Cheers. ...
written 4.9 years ago by paulparsons130

Latest awards to paulparsons

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Index MEDLINE/PubMed with Apache Solr
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Code for interactive web-based chromosome ideogram viewer?
Scholar 4.6 years ago, created an answer that has been accepted. For A: Specify Assembly for NCBI Entrez Query
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Specify Assembly for NCBI Entrez Query
Scholar 4.9 years ago, created an answer that has been accepted. For A: Specify Assembly for NCBI Entrez Query
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.

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