Category Archives: What’s the Answer?

WYP?

What’s The Answer? (where + how to get help online)

wyp_q_mark2_thumbnail1We started the the weekly “What’s the Answer?” thread to highlight various sources of interesting discussions related to bioinformatics around the internet. It was years ago–before communities like Biostar and others were well-trafficked and well-known. It’s been great to see these sources mature and draw diverse discussants from all over the world. What’s particularly helpful is that it’s not just the resource providers who give the answers now, as it used to be with the mailing list system at a given site. Now lots of end-users of tools can chime in about their experiences.

Recently a helpful pair of blog posts by Keith Bradnam summed up the helpful locations that exist now. The first post was: Where to ask for bioinformatics help online and listed a number of the locations we explore, and is taking suggestions for others as well. You should have a look at them, some we didn’t cover much here.

A second post offered guidance on how to ask properly: How to ask for bioinformatics help online. It’s really important to understand the community norms at these places. I find they can get very testy if they consider you off-topic for their forum, or if you are trying to ask them to do your homework. So you really should think about where and how you are asking for help. Sometimes you may be better off at a different site.

Anyway, since there are now so many mature sources of advice in this field, we are going to retire this topic as a weekly item. But our posts will still be here and searchable, so if there is a topic we’ve covered it will be available. But you should spend your time checking out the various places where the chatter goes on. And you should contribute to the answers when you know them. The proportion of consumers to contributers is often out of whack. A dedicated small bunch is very active, but we are all better off with more diverse contributors. Add your voice.

reddit_icon

What’s the Answer? (what’s up with the tardigrades?)

reddit_iconThis week’s discussion is different. But it’s a neat look at the issues of genome assembly, contamination, over-prediction and under-prediction. If you haven’t been following the drama, it began with the paper covered in this story by Ed Yong: Inside the Bizarre Genome of the World’s Toughest Animal. This group suggested that upwards of 17% of the tardigrade genome was imported from other species via horizontal gene transfer (HGT). Then another group who had been working on this species provided their pre-print on their work that came to a very different conclusion. Ed then wrote about that here: Rival Scientists Cast Doubt Upon Recent Discovery About Invincible Animals. They found much lower HGT.

Anyway, this week’s highlighted item from Reddit offers a look one researcher’s take on the whole thing, that comes to a third option.

academic_reddit Quick Look at the Two Manuscripts on Tardigrade LGT (igs.umaryland.edu)
submitted 4 days ago by rs4481887

This links to a blog post by Dr. Julie Dunning Hotopp. She’s worked extensively in lateral gene transfer, and has some excellent commentary on the whole thing. And there’s good discussion in the comments. It sounds to me that she’s suggesting there’s a porridge somewhere that’s just right. One of these was too hot, one was too cold.

It has been a fascinating story or publication, data access, analysis strategies, and gene transfer. I’m including the links to both papers below as well.

References:

Boothby, T., Tenlen, J., Smith, F., Wang, J., Patanella, K., Osborne Nishimura, E., Tintori, S., Li, Q., Jones, C., Yandell, M., Messina, D., Glasscock, J., & Goldstein, B. (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1510461112

Georgios Koutsovoulos, Sujai Kumar, Dominik R Laetsch, Lewis Stevens, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Aziz Aboobaker, & Mark Blaxter (2015). The genome of the tardigrade Hypsibius dujardini bioRxiv DOI: 10.1101/033464

SummitGeneEdit

What’s the Answer? (Dare we edit the human race?) #GeneEditSummit

SummitGeneEditThis week’s question is a biggie. And there’s no answer yet. But that is the topic of the National Academies big event this week, International Summit on Human Gene Editing. I have been glued to this for the whole time and didn’t spend much time looking for questions this week. And I’ll be watching the final day today. You can find the agenda and livestream at that link now, and the recordings will be available later.

A very good summary of the meeting so far came from STAT News today, and that’s where I got the title. So the closest thing you’ll get to an answer right now is that. And you will see that mostly there are just more questions at this point. Hat tip to Tim Caufield.

In that STAT piece, you will also see the reference to Sarah Gray’s powerful moment. It’s less than a minute, but it had me weeping at my desk. I had already heard Sarah and her son’s story on Radiolab. Hat tip to Michelle Meyer for that connection after Sarah’s comment:

In case you missed it, it’s hard to link to exactly where it is in the videos. It doesn’t have a way to get you to a spot like Youtube. So I’ve taken the clip out here. You can link to the full video collection at the National Academies site here. Go to Day 1, Part 3, 2:01:30 for the part with her comment for the best version. I just offer this short screengrab clip because I think that reading her comment doesn’t have the same impact and you should see it. Take a minute.

In case you can’t watch the video, the quote from STAT:

She implored the meeting, “If you have the skills and the knowledge to eliminate these diseases, then frickin’ do it!”

I have nothing to add to that, except to say I stand with Sarah.

Quick links:

Summit site: http://www.nationalacademies.org/gene-editing/Gene-Edit-Summit/index.htm

Agenda document:  http://www.nationalacademies.org/cs/groups/genesite/documents/webpage/gene_168809.pdf

Reference on the summit:
Reardon, S. (2015). Human-genome editing summit to sample global attitudes Nature DOI: 10.1038/nature.2015.18879

Biostars

What’s The Answer? (authorship heartbreak)

This week’s highlighted discussion generated a lot more chatter than many of them do. I didn’t see that coming at this site. But apparently it’s an issue that many groups have faced and had opinions on: what is the relative contribution of the wet lab vs bioinformatics side when it comes to the paper, and how to recognize that?


Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Forum: Do bioinformaticians often break molecular biologists’ hearts by being the first author?

Recently I knew a molecular biologist postdoc who was upset since she was placed by her boss as a second first-author in a paper that she wrote from scratch. Her boss put a bioinformatician/biostatistician as the first first-author, with a reasoning to the postdoc that she would not have anything if they take out the data processing part.

And it turned out that she is not alone. From this postdoc’s facebook, I learned that some of her friends admitted that they also experienced a very similar situation: being a molecular biologist, did all the labworks, wrote the paper, but put as a second author while the first one is a bioinformatician.

Apart from politics in the lab etc., I wonder if this is really quite common. If it is, don’t you think it’s quite unfair for the molecular biologist?

sentausa

It’s hard to assess from an anecdote what the real story was. I’m sure it was painful for folks involved. And, of course, at a heavily bioinformatics site, popular answers pointed out that often the bioinformaticians are the ones feeling neglected. But I thought it was interesting to highlight the tensions between folks on teams like this. And some pro-active awareness of this for people running labs might be in order.

It generated quite a range of comments. Some aimed at the publishing in general, some project related. Have a look.

 

Biostars

What’s the Answer? (career path)

This week’s highlighted discussion doesn’t actually have an answer. Yet. The idea is you provide the information, if you are or have been a postdoc in bioinformatics.


Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Forum: Quick four-question survey on bioinformatics postdoc career path

If you are in or have been in a bioinformatics postdoc, how did you get there:

http://bit.ly/bioinfopostdocsurvey

There is a related biostars question C: Change career path.

Sean Davis

I answered, despite the fact that my late 1990s postdoc may not be all that relevant to current students. It was well before there were any formal programs and educational tracks. It is a question I see over and over on all these forums that I read, and a little data collection might be illuminating. Anyway, go look at the short survey and help out if you have experience.

 

reddit_icon

What’s The Answer? (software poster advice)

reddit_iconThis week’s highlighted question is from the Bioinformatics subreddit. A simple question about advice for some poster design turned into quite the conversation about what people want from software posters

reddit question icon

need advice for poster about a bioinformatics software
submitted 7 days ago by Elendol

Hi,

I’m a first year PhD student in Bioinformatics. I’m creating a poster for the symposium of the department to present a software I developed.

There is no algorithm to discuss, no discovery, no findings as it’s mainly a data visualisation tool. The public will be biologists and bioinformaticians

I have problems to organise the abstract and the poster, do you have some advices / examples of posters “only” presenting a software. What are the important things to talk about, the things I don’t have to forget ?

I guess no one is really interested to read something about the implementation, software architecture and other developper’s stuff.

Thank you

So the discussion ensued about the role of the poster. And the role of the presenter. Whether to have code or not to have code. I was actually kind of amused at how deep people’s feelings were on some of these matters. Anyway, I thought it was a fun read. Have a look.

Biostars

What’s the Answer? (augmented reality in bioinformatics)

This week’s highlighted discussion turned out to be very popular. I was intrigued by the initial inquiry–but it evolved into a neat discussion of what sorts of visualizations might be interesting directions in the future.


Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Forum: Possible augmented reality tools for bioinformatics and current problems

Hi.

I was thinking about an application of augmented reality tools to help understanding bioinformatics problems. Although it may look like a useless thing to do (to have) could it actually be helpful for someone to have a tool that solve particular problems related to 3D-visualization using some augmented reality stuff?

If above statement is true could you give me some examples of such applications? I am considering all the possibilities because for me it looks like a good question to investigate.

It may be obvious from above but I would like to take similar topic for MSc thesis so all the suggestions are really welcome!

Thank you!

Peter Leontev

The protein structures part didn’t surprise me, of course. And while watching twitter this morning, this came flying over my feed:

There’s a comment over at Biostars from someone who put their ChIP-Seq data in Minecraft, and found it wasn’t particularly helpful. I loved the idea of watching cells divide, though. I was sort of surprised that nobody brought up the 3D Virtual Worm. And I added a couple of other thoughts too. It was all fun to think about, anyway. Add your thoughts if you have them. It’s nice to see a student considering future project ideas. Check out the chatter.

 

angry

What’s The Answer? (what frustrates you?)

angryOk, this week’s attempt to get at answers to big (and small) questions is not from one of the usual places that I do my question-mining. This came from Twitter. It started out as a request for some survey data among the bioinformatics/genomics twitterati. And it turned into a fascinating, raw, thoughtful, irreverant, and compelling read of the real issues out there. Also Mick Watson.

Clicking on the timestamp for the tweet will give you a glimpse into some of the chatter. But be sure to look at the actual answers for some really good ideas about what’s frustrating to researchers and people who are training others.

I was scanning through the results mostly focusing on the columns:

  • What problems running software if any do you most often encounter with this solution?
  • If you train students, please say what in your view is the biggest challenge for training students in bioinformatics?

Here’s a quick sample of what the data looks like:
what_frustrates_you

Some of it’s not new, of course. The number of times poor or inadequate documentation comes up…sigh.

poor_documentation

People want this. But few will pay for it or take it seriously. No, I’m not bitter. Really. 

The data is available for anyone to look at, over at FigShare. I want to take a close look one of these days with a nice cup of hot chocolate and think about some of the gaps here. I suspect there are some really informative nuggets. But I wonder if there are viable solutions.

Edit to add: This same data set generated a post by Keith Bradnam. He seems to have noticed the same thing.

We asked 272 bioinformaticians…name something that makes you angry: more reflections on the poor state of software documentation.

 

Reference:

Loman, Nicholas, & Connor, Thomas (2015). Bioinformatics infrastructure and training survey. figshare. http://dx.doi.org/10.6084/m9.figshare.1572287 Retrieved 15:19, Oct 20, 2015

UCSC Genome Bioinformatics

What’s the Answer? (keyboard shortcuts for UCSC)

This week’s solution is unusual. It didn’t come from my usual sources of questions. It came from twitter. It’s from the UCSC Genome Browser team. But it’s such a handy answer to a simple problem that it’s this week’s Answer post. So here’s my source of an answer to a ?

I had it in my files and forgot to try it out at first, but now I have. And I think there are several that I would probably use pretty often. But I know I use the web interface more than some people.

Anyway, try it out on some common tasks.

reddit_icon

What’s the Answer? (publication quality alignment images)

reddit_iconThis week’s highlighted question is from the Bioinformatics subreddit. And I’m using it because it made me laugh. I dare someone to name their alignment tool “Fancy Pants”. That said, it did provide links to a number of different tools that people might find useful, depending on the kind of thing you might want to do do make your stuff look niiiiiiiiice.

reddit question icon

Looking for publication quality alignment (‘fancy pants alignment’ are the words my colleague specifically used)

submitted  by CatsVansBags

Hey all- my colleague and I are looking for an alignment tool (software, website, etc) that makes beautiful looking alignments for publications. ClustalW is what everyone keeps suggesting and its nice but its not niiiiiiiiice. If anyone has any favorites, please fill me in, Thanks!

Some of the tools are things we’ve talked about before. Jalview and AliView, for example. But there are some others too. Have a look at the chatter and check ‘em out yourself if you need some alignments. Or, if you have other tools, suggest them.

{By the way, I am familiar with the tool called FancyGene. But it’s different.}