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Area 51 » Science

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Bioinformatics

Launched Q&A site for researchers, developers, students, teachers, and end users interested in bioinformatics.

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4  
Please do not use comments to answer these questions. This proposal is not part of a Q&A site, and the task at hand is to help define what is on and off topic for a site. Comments are here to help improve the questions; not to answer them. See What is the rationale for deleting answers? Thank you. – Robert Cartaino Apr 18 '17 at 3:30

6
votes
2
answers

I committed to beta: now what?

may 17 '17 at 15:56 Robert Cartaino 473
2
votes
1
answer

Can't upvote questions on area51 proposals on bioinformatics

may 7 '17 at 13:45 Robert Cartaino 473
4
votes
0
answers

Which topics of the following list; would be on-topic (or off topic) in bioinformatics SE? [closed]

may 4 '17 at 19:51 Always Confused 132
11
votes
1
answer

What counts as “200+ rep” in the commitment phase?

may 4 '17 at 18:42 Community♦ 1
12
votes
2
answers

What’s the focus of the site?

apr 19 '17 at 23:48 medbe 212

discuss this proposal

54 Example Questions (3 closed)

active newest votes
up vote 9 down vote
How to choose the best soft threshold value in WGCNA pacage of R. #bioconductor #clustering
added by prab4th Apr 15 '17 at 18:02
link
up vote 4 down vote
As a computer scientist, what books should I read to enter Bioinformatics? [closed]
added by Koo Zhengqun Apr 17 '17 at 15:20
link

closed as duplicate of What are the classical textbooks I should read as a newcomer to Bioinformatics? [closed] by Robert Cartaino Apr 18 '17 at 16:02

This question covers exactly the same ground as another question in this proposal.

I like this because the question is open-ended, but provides specificity in the questioner's background. The answers to "I am an X; what should I (read / do) to become more proficient in Bioinformatics?" will be different (and informative about the nature of Bioinformatics) depending on what X is. – gringer Apr 18 '17 at 12:43
1  
This proposal is about to undergo a final review, so for the purpose of defining the scope of this proposal, pruning out closely-related questions helps assure we have a sufficient breadth of subject matter to actually create this site. – Robert Cartaino Apr 18 '17 at 16:02
1  
The other question has been closed, so this no longer duplicates scope. – gringer Apr 18 '17 at 20:48
I understand they are not duplicate at all [1], although the phrasing could be changed to make the distinction clear. (As a not very experienced SE user, should I be concerned that this pruning might be responsible for previous attempts at a bioinfo SE failing? e.g. ppl may not feel appreciated, votes might be lost, scope might be decided too narrowly?) [1] a CS person would be directed to books heavy on the biology (or even not bioinfo at all, just "pure" biology). Classical bioinfo books, on the other hand, generally assume knowledge of Biology, and go to explain algorithms. – Leonardo de Oliveira Martins Apr 18 '17 at 21:37
Maybe someone could better rephrase this question. Going by the same reasoning, we would have many duplicate questions for different professions: biologists, graduate, software engineer, chemist, etc... Perhaps something like "I generally understand algorithms, what should I read to understand the specialized algorithms used in Bioinformatics?" – Koo Zhengqun Apr 18 '17 at 23:36
up vote 3 down vote
Why cufflinks quantifies some gene expression as null where other tools (e.g. HTSeq) give (sometimes very high) expression values?
added by Mitra Apr 18 '17 at 11:57
link
up vote 2 down vote
How to efficiently generate a random sample of alignments from a bam file?
added by bli Apr 18 '17 at 8:54
link
up vote 1 down vote
There are often multiple tools for the same purpose. How do you make choices in general? [closed]
added by medbe Apr 17 '17 at 19:41
link

closed as not a real question by Robert Cartaino Apr 18 '17 at 16:09

It's difficult to tell what is being asked here. This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form.

1  
Please be more specific about what problem you are trying to solve. The purpose of these questions is to help define the scope of this site, but I could drop this question into just about any community and it would seem to fit that site. Sometimes a questions can be so generic, it doesn't help define the scope of the site at all. – Robert Cartaino Apr 18 '17 at 16:09
up vote 1 down vote
How can I determine why so many of my sequencing reads are aligning outside my target region?
added by morgantaschuk Apr 18 '17 at 21:32
link
up vote 0 down vote
What is the tss_id attribute in some gtf files? How is it determined?
added by bli Apr 18 '17 at 8:55
link
up vote 0 down vote
Which programming languages have specific features that are useful for computational evolutionary biology?
added by wythagoras Apr 18 '17 at 16:48
link
Please be more specific about what type of feature set or problem you are trying to solve. Asking which language is useful in a broad context like this will likely become a "list your favorite programming languages" thread. – Robert Cartaino Apr 18 '17 at 17:05
1  
@Robert Cartaino, I changed "bioinformatics" to "computational evolutionary biology". Most bioinformatics modules/languages (e.g. Biopython) are more focused on DNA sequencing. I think this changed question would have only a few possible answers. – wythagoras Apr 18 '17 at 18:24
Thank you for the update. Let's see what the community thinks of it. – Robert Cartaino Apr 18 '17 at 18:43
up vote 0 down vote
How to design an algorithm that finds the begin of an mRNA string that codes for a protein in Python?
added by wythagoras Apr 18 '17 at 16:49
link
up vote 0 down vote
How can I phase a set of variants from a single individual using my read data?
added by sh4wn Apr 19 '17 at 14:43
link
up vote 0 down vote
How can I plot a phylogenetic tree in R or python, given that I have its newick representation as a string?
added by Leonardo de Oliveira Martins Apr 19 '17 at 21:43
link
up vote 0 down vote
Are there any novel algorithms developed for bioinformatics that are based on the Burrows-Wheeler transform, since it is so popular in the field?
added by Leonardo de Oliveira Martins Apr 19 '17 at 21:55
link
up vote -1 down vote
What is the most efficient way to download several FASTA files if I have a text file containing the accession numbers?
added by prab4th Apr 17 '17 at 9:27
link
Since we are now defining what and how should be good questions for the proposed site, it would be very helpful to accompany downvotes with a clear explanation for it. Ideally you should describe ways of improving the question. – Leonardo de Oliveira Martins Apr 18 '17 at 11:33
up vote -2 down vote
I have a set of aligned viral sequences. How can I check if some of them are recombinants?
added by Leonardo de Oliveira Martins Apr 15 '17 at 21:20
link
2  
Since we are now defining what would be good questions for the proposed site, it would be very helpful to accompany downvotes with a clear explanation for it. Ideally we should describe ways of improving the question. – Leonardo de Oliveira Martins Apr 18 '17 at 11:34
1  
Yeah, I don’t understand the downvotes at all. I think it’s a completely fine question. Unfortunately I have no more upvotes to give. – Konrad Rudolph Apr 18 '17 at 16:52
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