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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1answer
15 views

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 ...
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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 ...
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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 ...
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2answers
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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 ...
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1answer
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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 ...
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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
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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 ...
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1answer
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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 ...
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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 ...
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2answers
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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 ...
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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 ...
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0answers
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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, ...
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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 ...
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1answer
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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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0answers
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
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'...
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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 ...
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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
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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). ...
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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 ...
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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
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), ...
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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
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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
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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
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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
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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 ...
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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
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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 ...
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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
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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
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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 ...
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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 ...
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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, ...
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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)
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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. ...
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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 ...