User: navela78

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navela7830
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Posts by navela78

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Comment: C: Describe Your Architecture: Uniprot (2017)
... Yes we are still in the biking stage :) Thanks for your pointers. Just to clarify - We are not working in a clinical setting. The software will not store reads. It is supposed to store protein and gene sequences along with metadata like species, lineage, annotations, length, etc. Again, thank you ...
written 8 weeks ago by navela7830
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Comment: C: Describe Your Architecture: Uniprot (2017)
... Thank you so much! I really appreciate it. I have already spent couple of hours reading your answers. I work for a start-up and we do not have experience with data at this scale. I have been tasked to look into this big data management problem and maybe we will hire someone with more experience soon ...
written 8 weeks ago by navela7830
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Comment: C: Describe Your Architecture: Uniprot
... Hello, I have posted a new question: https://www.biostars.org/p/278519/ ...
written 8 weeks ago by navela7830
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Describe Your Architecture: Uniprot (2017)
... This question is related to https://www.biostars.org/p/64847/#278145 Asking it again because Jerven could not add to the original post .... What does the architecture of Uniprot look like today (Oct 2017)? How has it evolved? If you were to implement a software to store several hundreds of mill ...
genome written 8 weeks ago by navela7830 • updated 8 weeks ago by me560
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Comment: A: Sequence Data Management
... Thanks for your response Pierre. The number of metadata is large ... in the order of hundreds of millions. The complexity will be low. It will have simple things like name, length, start coordinate, end coordinate, unique ID. The only complex thing that may be there in the metadata is the taxonomic ...
written 9 weeks ago by navela7830
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Sequence Data Management
... hello I am working on a project to store and manage genome sequence data. Specifically microbial genomes. The tool should store several thousand genomes and need to find and extract sequences (contigs, genes, proteins) quickly. What is the best way to implement this? I saw this post but it is 5 yea ...
genome written 9 weeks ago by navela7830 • updated 2 days ago by Biostar ♦♦ 20
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Answer: A: Describe Your Architecture: Uniprot
... Hello I am wondering what the UNIPROT architecture looks like now after 5 years of further data explosion? Are you still using Berkley DB and lucene? Sorry I am new to this area ... I am also wondering how you store the sequence data ... do you upload it into the berkley db or maintain it as flat f ...
written 9 weeks ago by navela7830

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