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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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 ...
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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 ...
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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 ...
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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 ...
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1answer
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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 ...
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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 ...
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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 ...
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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 ...
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1answer
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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 ...
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2answers
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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?
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4answers
80 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'...
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1answer
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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 ...
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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, ...
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1answer
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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). ...
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2answers
45 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 ...
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3answers
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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 ...
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4answers
264 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), ...
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2answers
60 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 ...
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2answers
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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: ...
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1answer
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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 ...
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2answers
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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 ...
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1answer
43 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 ...
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1answer
25 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 ...
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1answer
40 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 ...
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1answer
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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 ...
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1answer
42 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 ...
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1answer
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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 ...
5
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2answers
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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 ...
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0answers
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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 ...
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4answers
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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 ...
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1answer
78 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 ...
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2answers
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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
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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 ...
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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 ...
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2answers
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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, ...
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3answers
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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)
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1answer
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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. ...
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3answers
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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 ...
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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?
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1answer
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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....
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3answers
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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 ...
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1answer
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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 ...
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Make tags [read-mapping] and [alignment] synonyms

As far as I can tell, there is no noticeable difference between the tags read-mapping and alignment. Three of the fifteen questions under these two tags use both tags, and the rest seem too similar to ...
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3answers
141 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 ...
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2answers
46 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 ...
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1answer
43 views

Replace sam and bam tags with a single sam-or-bam tag

The discussion in the recent suggestion to make sam and bam synonyms seems inconclusive with users falling on either side of the argument. I propose we instead remove both tags and create sam-or-bam,...
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368 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, ...
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5answers
100 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 ...
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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 ...
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1answer
111 views

Essential questions about our site [closed]

Looking for help I found this post about the beta sites essential questions that need to be answered. Now, that we will go to public beta soon, we could decide when to answer them: Are questions ...