Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 79k
Reputation:
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Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
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Google Scholar Page
Last seen:
14 hours ago
Joined:
9 years, 5 months 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: Question: Converting FASTQ to BAM by using Bowtie2
... heh, I don't even remember how I ended up with `=` signs, I believe they are valid to use, since the recipe does work. That's what's great about recipes. The code actually gets run by the website, the code is "alive" so to speak, errors that crash it out will get caught right away unlike "static" co ...
written 18 hours ago by Istvan Albert ♦♦ 79k
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Answer: A: Question: Converting FASTQ to BAM by using Bowtie2
... On the Bioinformatics Recipe website I have an example for how to use bowtie2: * in a nutshell you have to build an index for the reference then run the see other recipes here: * ...
written 20 hours ago by Istvan Albert ♦♦ 79k
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Comment: C: Retrieve many FASTA of the same gene from NCBI..
... What https://www.biostars.org/u/25721/ alludes to is that your answers seem to go off tangents that are not relevant here. "Click BLASTN, enter query sequence, paste into Word" etc instead, your answers should be more concept oriented. Here for example what you are trying to suggest is that one cou ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Answer: A: Bam header editing
... Sounds like what you need is to replace a readgroup where you overwrite all alignments with a new readgroup: samtools addreplacerg prints: Usage: samtools addreplacerg [options] [-r <@RG line> | -R ] [-o ] Options: -m MODE Set the mode of operation from one of over ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Comment: C: Can we consider Bioinformatics as a engineering discipline?
... traditional biology is descriptive, sentence driven, enumerative, dare I say "mechanistic" - this thing does this, that thing does that, but what if different combinations of "things" can give you the same "that"? There is no way to capture, model or understand those phenomena. in my opinion, trad ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Answer: A: Can we consider Bioinformatics as a engineering discipline?
... Bioinformatics is about information as the name aptly states (even though originally that was not the intent). Initially, "informatics" meant the use of information technology (computers) to process data of biological significance. But the more we know about how the cell operates the more we under ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Answer: A: Small dataset for data analysis in the own laptop
... Saccharomyces Cerevisiae has a genome size of a mere 12 million bp, it is also one of the most studied model organisms. Thanks to the small genome size, you can re-run just about any analysis on a laptop. Another common strategy, for say human size genomes is to find an experiment that also publis ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Comment: C: Are parasites good as model organisms?
... I haven't seen the original title but I will say that we can definitely learn a lot from parasites when it comes to the function of cells. Then what we learn could be put to good use. I think the title should reflect that message: what can we learn from parasites, or what are parasites good for etc ...
written 13 days ago by Istvan Albert ♦♦ 79k
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Answer: A: BWA error when aligning multiple files
... at least one of you fastq file pairs (among the many) uses an old school naming scheme where the read names are not identical across the pair. `29_1_1101_2537_1125/1` vs `29_1_1101_2537_1125/2` ...
written 14 days ago by Istvan Albert ♦♦ 79k
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Comment: C: SAM to BAM conversion problem after HISAT2.
... note how above you run samtools view out.bam which is empty so will, of course, raise an error. See what samtools view out.sam prints I think your BAM file is empty, for whatever reason, you would need to run the conversion again and see why it failed. I think it ran of out "somethin ...
written 14 days ago by Istvan Albert ♦♦ 79k

Latest awards to Istvan Albert

Great Question 8 days ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How To Learn To Build A Bioinformatics Oriented Web Site
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How To Learn To Build A Bioinformatics Oriented Web Site
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How To Learn To Build A Bioinformatics Oriented Web Site
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Picking A Programming Language And Where To Begin
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How Much Of The Genome Will Remain Un-Sequenced At A Given Coverage?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Picking A Programming Language And Where To Begin
Librarian 4 weeks ago, created a post with more than 10 bookmarks. For Table Of Contents To All Review Paper Compilations On Biostar
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How Much Of The Genome Will Remain Un-Sequenced At A Given Coverage?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How Much Of The Genome Will Remain Un-Sequenced At A Given Coverage?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Redundant @Sq Lines In Bam File
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Great Question 8 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Great Question 9 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Great Question 11 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Scholar 3 months ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools

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