Admin: Istvan Albert

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Istvan Albert ♦♦ 85k
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Location:
University Park, USA
Website:
https://www.ialbert.me/
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Google Scholar Page
Last seen:
46 minutes ago
Joined:
11 years, 1 month ago
Email:
i************@gmail.com

I have published research works in the fields of granular matter physics, network sciencemachine learninguser interfaces and bioinformatics. But above all I like to create useful systems. I  enjoy the process of designing and implementing web based services that stand the test of time. My current project that I dedicate most my time to is an e-book on genomic data analysis:

  • The Biostar Handbook - it is modeled by the content on this site and is a comprehensive guide for beginning bioinformaticians.

I am the  maintainer of this site:

  • Biostar Q&A platform  more of a jack-of-all-trades:  lead developer, interface designer, database manager, sys admin, dev-ops etc. whatever needs to be done.

Currently I work as a  Professor of Bioinformatics at Penn State. Within that position I serve in various roles:

Posts by Istvan Albert

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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... This particular paper was submitted via ENA (European Nucleotide Archive) and perhaps before the paper was accepted. This might be a reason it is not properly crosslinked in PubMed. Going through ENA does show the paper (you have to click Show under Publication tab) https://www.ebi.ac.uk/ena/bro ...
written 3 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... NCBI often boggles the mind. What if one produces 500 SRA experiments? Should they now list each number separately in the paper? I perhaps understand the sentiment, they try to discourage people from linking to the bioproject *alone* as the main entry point. ...
written 3 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Elink to get PMID associated with a BioProject or SRA entry
... the publication is embedded in the information when fetched as XML: efetch -db bioproject -id PRJNA257197 -format xml > out.xml extract the pubmed id cat out.xml | xtract -pattern ProjectDescr -element Publication@id prints 25214632 which then you can fetch one by one (or as li ...
written 3 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Funny name or unsublte hacker?
... Amusing development in the story, I wrote to ncbi asking why that folder is there, 4 days later I got the following response: > Thank you for the report. I do not see a directory called ProdigalHack > in https://ftp.ncbi.nlm.nih.gov/genomes/ Maybe we removed it? I have > not heard of a pr ...
written 7 days ago by Istvan Albert ♦♦ 85k
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Answer: A: NCBI Viral Genomes Resource
... Try these tools: NCBI Datasets: https://www.ncbi.nlm.nih.gov/datasets/ or possibly: https://github.com/kblin/ncbi-genome-download ...
written 8 days ago by Istvan Albert ♦♦ 85k
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Comment: C: two-sample test with cut-off measurements
... I would recommend this to be posted on the Bioconductor Support site or the Statistics Stackoverflow. It is a very specific question on the statistical interpretation and validity of the model, rather than the bioinformatics principles. ...
written 8 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Download ncbi database with filezilla
... I have Filezilla and gave it shot, looks to works just fine, paste URL in the host, then Quickconnect As https://www.biostars.org/u/18713/ mentions FTP might be blocked by the network firewall. See if your command line still works on the current system (network). ...
written 8 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Paper: Ten simple rules for biologists initiating a collaboration with computer
... Perhaps number 5 I would phrase in terms of learning about the scalability/limitations/tradeoffs of the various algorithms instead of specifically calling out the speed as a bottleneck. Many other bottlenecks may be present, having a sense of the computational complexity would help the communicati ...
written 8 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Paper: Ten simple rules for biologists initiating a collaboration with computer
... Hah! I am very pleased that this made into it. I have always made a strong point in the classroom of how absurd is to tie "reproducibility" to a specific version of a software. Even beyond that, if results only hold when using TopHat but not HiSat perhaps that outcome is dubious to begin with (unles ...
written 8 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Paper: Ten simple rules for biologists initiating a collaboration with computer
... Let me list the rules here for easier reference: 1. Do not try to turn them into biologists 2. Do not judge knowledge gaps 3. Learn how computers store data and format information in a computationally friendly way 4. Describe your data in a way that facilitates collaboration 5. Learn if you should ...
written 8 days ago by Istvan Albert ♦♦ 85k

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