Admin: Istvan Albert
Istvan Albert ♦♦ 85k
- Reputation:
- 85,070
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- 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 science, machine learning, user 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:
- Director of the Bioinformatics Consulting Center at Penn State
- Bioinformatics instructor
- Researcher and tool developer GeneTrack, and a few others
Posts by Istvan Albert
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... 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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... 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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... 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
1
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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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... 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
1
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... 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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... 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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137
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... 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
0
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... 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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