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.

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26
votes
4answers
798 views

Is there a large enough community to sustain this site?

Update: This site has passed the final evaluation! Barring any technical delays, Bioinformatics SE should go public sometime this week. Great work everyone! (original post) Spread the word. In less ...
22
votes
8answers
637 views

Accepting Nominations — Who should moderate this site? [duplicate]

Ideally, Moderators♦ are elected by the community, but until the community is large enough to hold a proper election, we will be appointing three provisional Moderators to fill those roles. We need ...
20
votes
3answers
215 views

What sort of questions are appropriate for Bioinformatics SE?

I have spent a lot of time on StackOverflow and am pretty familiar with the types of questions that are and are not allowed on the site. I am a little unsure as to how well the strict question rules ...
19
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2answers
130 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 ...
18
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0answers
105 views

Let’s standardise some tags

Let’s standardise some tags. For instance, there are already two competing conventions at work: rna-seq scrnaseq Either both should use a dash, or none should. I propose the slightly more readable ...
15
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3answers
224 views

Please refrain from closing proper but imperfect questions so quickly

I have been thinking about this for a while. This recently on-hold question really touches my nerve. The question is put on hold due to being too "broad". I will use it as an example to explain my ...
15
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1answer
201 views

What to do with answers inspired by BioStars?

Out of curiosity I followed the first of Pierre's BioStars links from the comments on the FASTA lengths question, and noticed that our currently accepted answer bears a strong resemblance to this ...
14
votes
3answers
143 views

How do we feel about questions that are essentially about text parsing?

A lot of the daily tasks of a bioinformatician can be boiled down to simple text parsing. Yes, we will be dealing with text files containing some form of biological data, but the answer might not ...
14
votes
2answers
155 views

Should we allow questions about biology?

How do we feel about questions about biological principles that can be confusing to a bioinformatician with no background in biology? While purely biological questions should, I think, be off topic ...
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 ...
11
votes
2answers
145 views

Computational biology but not gene sequences?

I see that this site is focused on sequencing and genomics. I'm wondering if other fields that combine computations and biology are on-topic. Such as: molecular dynamics simulations, analyzing 3d ...
10
votes
3answers
106 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 ...
10
votes
1answer
95 views

Is it okay to write a post Introducing a tool?

I have just developed a new bioinformatic tool and I was simply wondering whether it is okay to write a post introducing the tool?
10
votes
1answer
91 views

Are we supposed to delete comments, once the issue has been resolved?

Sometimes a comment, leads to the answer (or question) update. In such case the comment is not relevant anymore, since it addresses a resolved issue. Are we supposed to delete comments like this? E.g. ...
10
votes
3answers
135 views

Serving as a “support forum” for specific tools

One of the nice features of biostars is that the site is open to people using it as a forum for supporting their own tools (i.e., as a replacement for a tool-specific email list). The tool authors ...
10
votes
2answers
75 views

Q&A-Style Answering Own Question

Since the site is in beta, and the idea is to develop a core of high-quality questions: should we be posting what we think are good questions which we ourselves know the answers to? For example, I ...
9
votes
4answers
274 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), ...
9
votes
1answer
106 views

Testing the boundaries of good questions?

In general, if you are unsure whether a question is the sort of thing we are going to want to see here, is it better to ask it on the main site and see if it gets closed, or enquire on meta first if ...
9
votes
1answer
78 views

General guidelines on creating tag synonyms and naming (personal opinions)

Recently, there have been a few threads on creating tag synonyms. I think most of these are not really synonyms. The following shows my thoughts about what are synonyms and what are not. I will also ...
8
votes
3answers
77 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 ...
8
votes
3answers
133 views

Migrating bioinformatics questions from other SE sites

There are a host of Bioinformatics questions on StackOverflow, CrossValidated, and probably other SE sites as well. Many of these questions would now be better placed here than on the site they were ...
7
votes
3answers
176 views

Interacting with other Q&A communities

When the proposal of Bioinformatics started there was a discussion in Biostars about the this site (and SE in general compared to Biostars). Some of the points raised are: Unfriendly community, ...
7
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2answers
387 views

Please stop cross posting behavior

Please stop cross posting behavior from biostars.org, where new questions are immediately transferred to this site. If you think you need this to boost your question count over the required threshold, ...
7
votes
1answer
127 views

Is it okay to ask questions regarding being a bioinformatician?

I was wondering if the Bioinformatics SE is a good place to post questions relating to the process of research in bioinformatics. Example: What is the proper way to format a PK/PD model for a ...
7
votes
1answer
76 views

How much this site is/ going to be on-topic to bio student lacking a proper IT and stat base?

I felt like if anyone have to learn bioinformatics in the 'proper' way, conceptually; then a base of statistics, data-modelling and computer-programing is a prerequisite. But biology students of most ...
7
votes
1answer
27 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 ...
7
votes
1answer
89 views

Are stories useful for bioinformatics questions?

I've just had a look at the fastest FASTA/FASTQ question, and felt that it was a bit lacking in substance. It was an answerable, specific question, and all the answers seem to concentrate on a single ...
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 ...
6
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4answers
83 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 ...
6
votes
1answer
51 views

Make tags [mapping] and [read mapping] synonyms

The topic of read mapping is a sufficiently distinct subset of the more general class of sequence alignment topics to warrant a dedicated tag. However, we should collapse ...
6
votes
0answers
64 views

Standard language for comments asking for an improved question?

One of the first things I needed to learn when coming to SO for the first time was how to ask a good question. I suspect I'm not alone in this. I was fortunate to have responses to my first (poorly ...
5
votes
2answers
88 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, ...
5
votes
5answers
101 views

Make tags [sam] and [bam] synonyms

SAM and BAM are effectively plain-text and binary representations of the same alignment format. I'd argue these terms should be synonyms. UPDATE: It doesn't look like we've reached a consensus, but I ...
5
votes
2answers
85 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
97 views

Questions about commercial products where there are official support channels

Though inspired by this question, this tends to come up more often in relation to CLC Workbench. On occasion, people using commercial closed-source packages will post questions about using said tools ...
5
votes
2answers
94 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 ...
5
votes
3answers
161 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 ...
5
votes
2answers
61 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 ...
5
votes
1answer
28 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 ...
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 ...
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 ...
5
votes
1answer
43 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 ...
5
votes
1answer
44 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 ...
5
votes
0answers
57 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 ...
4
votes
3answers
123 views

Should the first go an answer or comments?

I personally believe that community should offer the answer for the question before any other (even relevant) comment. I opening this thread, because one of the most upvoted answers is starting with ...
4
votes
2answers
44 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 ...
4
votes
2answers
47 views

Tag [file-formats] or [data-formats] to replace [formats] tag

As of now, 5 questions have been tagged with formats and since bioinformatics in practice is 80%+ file format conversion, we can expect many more such questions! I ...
4
votes
2answers
46 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 ...
4
votes
1answer
52 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 ...
4
votes
1answer
27 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 ...