User: Mitch Skinner

gravatar for Mitch Skinner
Mitch Skinner660
Reputation:
660
Status:
Trusted
Location:
Emeryville, CA
Last seen:
4 years, 8 months ago
Joined:
10 years, 3 months ago
Email:
m****@arctur.us

Posts by Mitch Skinner

<prev • 32 results • page 1 of 4 • next >
1
vote
2
answers
3.3k
views
2
answers
Answer: A: why aren't relational DB's used more for genomic data?
... Aside from what you and RamRS mentioned, the fact that you can transfer BAMs without an ETL process is convenient.  Also, there are some hybrid approaches: at one place where I worked, they built a postgres foreign data wrapper for BAMs, so you could query them with an SQL select (and do joins betwe ...
written 5.7 years ago by Mitch Skinner660
1
vote
2
answers
2.0k
views
2
answers
Answer: A: Jbrowse: importance of draw-basepair-track.pl
... The original motivating application was to show patterns of base pairing in RNA secondary structures. ...
written 5.8 years ago by Mitch Skinner660
3
votes
3
answers
3.3k
views
3
answers
Answer: A: java script multiple sequence alignment viewer
... There's a GSOC student, Sebastian Wilzbach, working on a JS MSA viewer, mentored by Tatyana Goldberg.  This is his blog, which has some links to demos: https://sebi.wilzbach.me/blog/ and this is the code: https://github.com/greenify/biojs-msa-amd ...
written 6.3 years ago by Mitch Skinner660
3
votes
3
answers
10k
views
3
answers
Answer: A: List Of File Formats Used In Bioinformatics?
... I often end up working from the UCSC file format description page. I don't think there can be a comprehensive list, because people are coming up with new formats all the time. ...
written 8.0 years ago by Mitch Skinner660
5
votes
2
answers
2.3k
views
2
answers
Answer: A: Which Javascript Framework To Use In Building Ui Widgets For Biology
... There are a lot of javascript frameworks; besides jQuery and ExtJS, the big ones I've looked at closely are dojo, YUI, Google's closure library, and prototype.js. And there are a bunch of others that I haven't really looked at. jQuery's roots are in adding a bit of interactivity to a server-generat ...
written 9.0 years ago by Mitch Skinner660
1
vote
4
answers
2.6k
views
4
answers
Answer: A: The Myriad Ruling - What Do Gene Patents Now Mean To Bioinformatics?
... I don't know if anyone really knows at this point. In case you haven't seen it, there's another detailed post on Genomics Law Report about this latest ruling: Pigs Return to Earth: Federal Circuit Reinstates Most—But Not All—of Myriad’s Patents ...
written 9.2 years ago by Mitch Skinner660 • updated 7.4 years ago by Giovanni M Dall'Olio27k
0
votes
4
answers
16k
views
4
answers
Comment: C: What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordin
... Also: the "interbase" interpretation of zero-based, half-open intervals makes it easier to describe indels. ...
written 9.6 years ago by Mitch Skinner660
0
votes
4
answers
16k
views
4
answers
Comment: C: What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordin
... Also: Keith James is totally right. But it's not just for circular genomes: flybase has some features that are in negative coordinates (don't know for sure why; I believe they're chromosome bands that have been mapped to locations before the sequenced region). ...
written 9.6 years ago by Mitch Skinner660
1
vote
4
answers
16k
views
4
answers
Comment: C: What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordin
... Great answer. I don't buy the "our brains are trained to think in 1-based, closed systems" argument, though. That may be true, but I don't think it's relevant. In my experience, it's rare to have features that start at the origin. That means that human beings hardly ever have to count from the o ...
written 9.6 years ago by Mitch Skinner660
2
votes
7
answers
8.3k
views
7
answers
Answer: A: Bio-Javascript?
... The JBrowse code is maybe 85% JS. One of my longer-term goals is to take any generally-useful JS code in JBrowse and split it out into a library. I think some of the data structure stuff, the NCList code and the trie code, might be useful elsewhere. That code might need some changes to be useful o ...
written 9.7 years ago by Mitch Skinner660

Latest awards to Mitch Skinner

Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: List Of File Formats Used In Bioinformatics?
Appreciated 7.3 years ago, created a post with more than 5 votes. For A: Which Javascript Framework To Use In Building Ui Widgets For Biology
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: List Of File Formats Used In Bioinformatics?
Appreciated 9.0 years ago, created a post with more than 5 votes. For A: Which Javascript Framework To Use In Building Ui Widgets For Biology
Teacher 9.0 years ago, created an answer with at least 3 up-votes. For A: Which Javascript Framework To Use In Building Ui Widgets For Biology
Appreciated 9.7 years ago, created a post with more than 5 votes. For A: Snp Position Problem
Good Answer 9.7 years ago, created an answer that was upvoted at least 5 times. For A: Snp Position Problem
Teacher 9.7 years ago, created an answer with at least 3 up-votes. For A: Snp Position Problem
Teacher 9.9 years ago, created an answer with at least 3 up-votes. For A: Modelling The Conservation Of Genome Positions
Appreciated 9.9 years ago, created a post with more than 5 votes. For A: Modelling The Conservation Of Genome Positions
Good Answer 9.9 years ago, created an answer that was upvoted at least 5 times. For A: Modelling The Conservation Of Genome Positions
Teacher 10.0 years ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Appreciated 10.0 years ago, created a post with more than 5 votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Good Answer 10.0 years ago, created an answer that was upvoted at least 5 times. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Appreciated 10.2 years ago, created a post with more than 5 votes. For A: What Is The Quickest Algorithm For Range Overlap?
Teacher 10.2 years ago, created an answer with at least 3 up-votes. For A: What Is The Quickest Algorithm For Range Overlap?
Appreciated 10.2 years ago, created a post with more than 5 votes. For A: Code Golf: Digesting Fasta Sequences Into A Set Of Smaller Sequences
Teacher 10.2 years ago, created an answer with at least 3 up-votes. For A: Code Golf: Digesting Fasta Sequences Into A Set Of Smaller Sequences
Commentator 10.3 years ago, created a comment with at least 3 up-votes. For C: Code Golf: Mean Length Of Fasta Sequences
Good Answer 10.3 years ago, created an answer that was upvoted at least 5 times. For A: Code Golf: Mean Length Of Fasta Sequences
Teacher 10.3 years ago, created an answer with at least 3 up-votes. For A: Code Golf: Mean Length Of Fasta Sequences
Appreciated 10.3 years ago, created a post with more than 5 votes. For A: Code Golf: Mean Length Of Fasta Sequences

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1471 users visited in the last hour