Questions tagged [discussion]
The question you're asking is designed to solicit opinions or best-practices on a particular topic, with the goal of reaching community consensus.
82
questions
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vote
1answer
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Vote to undelete question … and rationale
I triggerd a vote to undelete a question entitled
I have used TER to break the long bonds of a chain in my PDB
The question is here, deleted by the OP after it was answered by a member of the site ...
3
votes
1answer
31 views
Duplicate OPs and OP deletion of response postings
There was a recent issue on Bioinfo SE here on a question about compiling gromacs for CPU or GPU (below).
It appears a question was deleted together with @MatteoFerla's response and one question ...
2
votes
0answers
14 views
UniProt survey: Tell us what protein information is important to you
Please consider filling in this survey, on behalf of UniProt:
As biological data is growing at an exponential rate, we also have to prioritise the protein information we present. In order to help us ...
3
votes
2answers
45 views
Should something be done about frozen “main” chatroom?
I have noticed that the "main" chatroom for this site has been frozen. By the main chatroom I mean the room which was created when the site was created with the description "General ...
0
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1answer
38 views
Why does @gringer have a wiki tag?
Whilst editing the sites wiki tags I noted that @gringer was listed, alongside including formal technical nomenclature such as population genetics, allele frequencies, haplotype networks, synonymous ...
4
votes
1answer
41 views
I'm a bioinfo software developer, and I would like to use bioinformatics SE as the main platform for Q&A
I'm an author of bioinformatic software and I would like to use this stackexchange as the main platform for questions and answers (indicate this in the README). The software is recent and there is no ...
2
votes
1answer
38 views
Importance of protecting questions
A new member has responded to a "SARS-CoV-2 synthetic origin" questions here and here with a "human origin" opinion expressed in a verbose, aggressive and non-technical manner.
I have now protected ...
1
vote
1answer
32 views
Adverts on Bioinfo SE
There is currently, essentially an advert on Bioinfo SE in another disguise here. Is there any fast-track system for removing it without the standard "close vote" system?
The "close vote" system ...
2
votes
2answers
58 views
Should we allow questions about the coronavirus?
As the flood of information, from around the world, comes in concerning the pandemic; should we create a coronavirus-bioinformatics tag and try to apply the principals of bioinformatics to it? This ...
3
votes
2answers
61 views
Bioinformatics, biostatistics and computational biology
I am wondering how others define the boundaries between bioinformatics, biostatistics, and computational biology.
In academic setting these three are treated as more or less equivalent terms or as ...
3
votes
2answers
33 views
“Synthetic” instead of “man-made”?
A question on Bioinformatics SE is about the possibility of coronavirus having been engineered in the lab and the question title includes the phrase "man-made", which, in my opinion, is an example of ...
2
votes
0answers
20 views
2019: a year in moderation
It's New Year's Day in Stack Exchange land...
A distinguishing characteristic of these sites is how they are moderated:
We designed the Stack Exchange network engine to be mostly self-regulating, ...
5
votes
1answer
36 views
Is asking about publishing in bioinformatics on topic?
I have a question about how to present bioinformatics methods for publishing in a paper. I tried asking it on Academia, but it was off topic there. Would it fit here?
More generally, would questions ...
2
votes
1answer
19 views
How to encourage/create effective tagging protocol
I have seen a few questions where people want to do something like convert a file, or they ask a question about a specific programming tool. Then they don't tag the post with the programming language ...
1
vote
0answers
22 views
Microbiome analysis tags needed!
We analyze the human microbiome using 16s sequencing. I couldn't find a single relevant tag for my question!
Tags Needed
General
16s
microbiome
microbial
taxonomic-assignment
16s-sequencing
dada2
...
2
votes
0answers
9 views
Synonymise [alignment] and [sequence-alignment]
While asking a question here, I noticed that alignment and sequence-alignment both exist. They appear to be synonymous; indeed, the alignment description reads, in its entirety:
These questions are ...
4
votes
2answers
187 views
Take care when deleting other people's writing
On finswimmer's answer to “samtools mpileup skipping read” there was previously a discussion in the comments re the (now corrected) overly wide claim that ...
2
votes
0answers
27 views
Propose new tags for the COMBNE community
I asked a question yesterday regarding the posting of questions related to COMBINE standards and got a positive answer. However in order for a reader to filter questions related to specific COMBINE ...
5
votes
0answers
59 views
Proposing new tag for the Bioinformatics channel
I am a synthetic biologist working heavily on the modeling of genetic circuits and the development of software for bioinformatics. Many researchers and software developers within bioinformatics rely ...
2
votes
0answers
29 views
Would this be a suitable community to post Q&As related to the COMBINE community?
I'd like to inquire about using the bioinformatics exchange to post COMBINE related questions. COMBINE, as describe in Wikipedia is: "COMBINE, the COmputational Modeling in BIology NEtwork, is an ...
4
votes
1answer
57 views
Would this be a good community for SBOL Q&A?
The Synthetic Biology Open Language is an open representational standard for encoding biological designs. As this community has been growing, it has been trying to figure out a better way than FAQs to ...
3
votes
2answers
75 views
When can we get out of the Public Beta?
We have been in the beta for more than 700+ days. What is the procedure and requirements to get out of the Beta stage?
3
votes
4answers
84 views
It's a bad idea to delete answers that include criticism towards the question
I recently answered a question which was promptly deleted by a mod, I realized now. I know I am new in this site, but I have been a long time user of SE sites and I think this decision is flawed. Here'...
2
votes
1answer
36 views
Proposal: remove [filtering] tag, replace with [quality-control] when appropriate
As of 2019-01-28, there are 16 posts tagged with [filtering]. This is an ambiguous and, at least in some cases, unhelpful term. Some of these posts are about ...
7
votes
0answers
33 views
2018: a year in moderation
It's New Year's Day in Stack Exchange land...
A distinguishing characteristic of these sites is how they are moderated:
We designed the Stack Exchange network engine to be mostly self-regulating, in ...
1
vote
1answer
21 views
RStudio tag addition
I found myself asking an RStudio specific question. The question is more about how a function works within the infrastructure of the software as opposed to general use of R or of the package (Seurat). ...
4
votes
2answers
48 views
rtag suggestion
I feel like we should sort out tags related to graphics. Right now there tags
visualization, plotting, figure-explanation + tool/package specific like ggplot2.
I identify three distinct problems ...
10
votes
3answers
110 views
Improving the site after 1 Year!
In 10 days we will be celebrating 1 year since the launch of the site!
I think it is a good time to discuss and review how to improve the site, talk about things that are working well and things that ...
9
votes
4answers
278 views
Should we relax the requirement for disclosing affiliation on the site?
There is a general rule on the Stack Exchange network that states that if you post an answer suggesting something you are involved with (e.g. a tool you wrote or a blog post you authored or whatever), ...
5
votes
2answers
62 views
Is it appropriate to ask for method papers on specific topics?
Is it appropriate to ask questions here that fall into the literature survey realm?
Some of the bioinformatics citation trails are a rats nest and it can be difficult to find appropriate methods ...
3
votes
2answers
37 views
Divide tags by technology and target application?
Reviewing an edit I realized we have some duplicated tags or at least somehow redundant.
We have scrnaseq, rna-seq and single-cell.
Some numbers:
scrnaseq: 25 questions
scrnaseq & rna-seq: ...
5
votes
1answer
29 views
Would questions on whole cell modeling get answers at this site?
I am self-learning about whole cell modeling, specifically An introduction to whole-cell modeling and Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models. While my background ...
4
votes
2answers
46 views
Migrating bioinformatics questions from the Bioinformatics SE chat
There's a little bit of frustration in chat with regards to people asking questions that would be better asked in the main site. See here, for example. Some people can be encouraged to re-ask the ...
5
votes
1answer
46 views
Are questions about the start point for a future career in bio-informatics on topic?
I am a math undergrad student and I'm highly interested in applications of mathematics to biology, medicine and health issues. However, my knowledge about bioinformatics is very limited. I did take a ...
7
votes
1answer
29 views
Are questions looking for help to find data on topic?
There are some questions1, 2 about finding data suitable for an experiment or validate a method.
Are those question on topic?
I was going to post a new one but then I thought that it might be too ...
5
votes
1answer
47 views
Are electrophysiology questions on topic?
As a mod on Bio and CogSci I am faced with quite some posts that are overlapping in all three fields. In the field of Bioinformatics I see a lot of questions (relatively spoken, as the absolute number ...
4
votes
1answer
31 views
Are (brain) imaging signal processing questions on topic?
So as an example, here 's a brain imaging signal processing question on CogSci. Although this question is well-prepared and on topic there, it will very likely never receive an answer.
This type of ...
5
votes
1answer
43 views
What do you think about a tag for meta discussion about the state of the profession?
I was searching for a tag earlier to add to my question here:
What happens if a major bug is discovered in a bioinformatic package that has been used in published literature?
I wasn't really able ...
4
votes
1answer
28 views
Are questions about analyzing and/or processing human/disease data on topic?
I'm tasked with obtaining some data about chronic disease on an human population. One of these is to identify people with a chronic disease from the data set. Since chronic diseases definition varies ...
6
votes
2answers
101 views
Closing because a question is cross posted?
A question has been closed as off-topic, and the moderator who closed said in a comment:
This is already receiving sufficient attention on biostars. Giving it further attention here would be a waste ...
19
votes
2answers
135 views
Community promotion ads
Shall we start a small advertising campaign?
Some Stack Exchange communities vote on “community ads” — banners that link to other resources related to the topic. Highly voted proposals get free ad ...
6
votes
4answers
84 views
Should pure statistics questions be on topic?
This question was prompted by differential gene expression complex design no replicates.
While that question isn't very clear, it seems to be essentially asking for help on applying statistical ...
3
votes
1answer
79 views
Where are the bioinformatics questions in other SE sites? (Community wiki)
Subject: This page is specified for discussion for feature development to link this site with other sites those too containing bioinformatics question.
Related: should we import questions from ...
5
votes
2answers
89 views
Are questions about installing bioinformatics tools on topic?
Should we allow questions asking for help installing specific tools? Some of the tools that are commonly used in bionformatics are non-trivial to install. They can require other packages, environment ...
5
votes
3answers
165 views
[alignment], [sequence-alignment], [read-alignment] and [msa] tags
Let's decide here on the status for different tags related to alignment.
There are two groups of questions.
One is related to pairwise and multiple sequence alignments and algorithms. This field is ...
14
votes
0answers
172 views
Moderator Pro Tem Announcement
Throughout the beta, we need members from the site whose focus is to engage the community, both in community-building issues and site management. That's why we select a few members from each community ...
5
votes
2answers
90 views
Should we be asking OPs to accept answers?
I have been seeing a lot of questions on here with answers, but most don't seem to have accepted answers (the check mark thing next to the answer comment). Based on my (limited) experience with SO, ...
0
votes
3answers
97 views
Should we allow questions where the title is not a question?
I think there are too many entries where the title is not a question.
Related discussions:
How do I write a good title?
Should question titles be phrased as questions? (A straw poll)
3
votes
1answer
41 views
Should [benchmarking] and [performance] tags be synonyms?
I just created a "performance" tag for this question.
I went to see if this tag could be added to other questions, and thought about this one, that happens to already have a "benchmarking" tag.
...
8
votes
3answers
79 views
What do we do with [software-recommendation]?
software-recommendation seems like a highly questionable tag to me, yet it’s collecting questions.
On other Stack Exchange sites, most notably Stack Overflow, software recommendations are explicitly ...
