User: tim.gallengor

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United States
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3 years ago
Joined:
3 years, 10 months ago
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Posts by tim.gallengor

<prev • 8 results • page 1 of 1 • next >
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Paxtools java library issue
... I am new to Paxtools and am going through the Paxtools Developer documentation. In practicing with Paxtools java library I have come across a couple issues. Any help/advice would be appreciated. 1.) I get an undefined method error when using getRDFId() on a BioPAXElement object. Other methods from ...
paxtools biopax written 3.1 years ago by tim.gallengor10
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BioPAX L4 Release?
... Is anyone familiar with when BioPAX 4 might be released? Curious as I saw that SBML may be easier to work with future BioPAX. ...
pathway biopax sbml written 3.1 years ago by tim.gallengor10 • updated 3.1 years ago by cannin250
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Comment: C: Best programming language for pathways and genomics?
... Thank you, I think I am going to go with python. Also, it seems like a good general language as well. ...
written 3.8 years ago by tim.gallengor10
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Best programming language for pathways and genomics?
... I am new to bioinformatics and programming. My background is in physiology, and I am looking to learn a programming language that can easily work with pathway and genomic data. Working with BioPAX XMLs and NGS VCFs seems to be the direction I am going in. What would be the best programming language ...
genome pathway python written 3.8 years ago by tim.gallengor10 • updated 3.8 years ago by BOC Sciences0
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How does Reactome format pathways in BioPAX?
... I am new to bioInformatics, and am trying to build some molecular pathways. I would like to make pathways that can merge with those in Reactome. I have been importing Reactome BioPAX networks into Cytoscape and I am confused as to how they format nodes and edges. For example, a single edge may be ju ...
pathway reactome biopax written 3.8 years ago by tim.gallengor10 • updated 3.7 years ago by Biostar ♦♦ 20
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Comment: C: how to obtain detailed pathways?
... Those annotations seem really useful! Although, I'm not sure how to get them, as I am using cytoscape 3.2.1, and I can only find descriptions on node attribute browser by looking at earlier versions of cytoscape. Do you know of another way to get these files? I have not used BioPAX before, but am lo ...
written 3.9 years ago by tim.gallengor10
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Comment: C: how to obtain detailed pathways?
... Yeah, that's a pretty neat feature, but still doesn't contain the information I need. For example, when importing Reactome pathways with ReactomeFIPlugIn, usually only gene entities are imported, not molecules. I end up exporting the table to mySQL adding additional entities and annotations, and the ...
written 3.9 years ago by tim.gallengor10
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how to obtain detailed pathways?
... I am new to bioinformatics and have a problem that I am sure almost everyone has faced or is facing. I know that my question is an over simplification, but any pointers in the right direction would be much appreciated. I would simply like to query (compare/contrast/word search/etc.) multiple biolog ...
pathway string reactome cytoscape kegg written 3.9 years ago by tim.gallengor10 • updated 3.9 years ago by AndreiR50

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