Category Archives: What’s the Answer?

What’s The Answer? (genomics is not special, stop reinventing the wheel)

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). Every Thursday 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.

This week’s highlighted Biostar post is one of the most interesting ones I’ve seen in a while. It started with a provocative premise, and this provoked a number of really fascinating responses and discussion. To lure you over there, here’s a tweet that captures the initial post:

(and this generated some chatter on twitter, if you follow the time stamp you can see that)

One of the response resounded across the genoscenti as well:

I think those short summaries are better than me bringing the post over here like I usually do. You should read the whole thing in situ, with the responses. So just go over from the links in the tweets, or from here.

Heh. This is what’s great about forums. This is way better than you get in the stuffy mainstream literature (with the except of Dan Graur).

What’s The Answer? (mobile bioinformatics apps)

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). Every Thursday 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.

This week’s highlighted discussion is about mobile apps. The original post sought some suggestions on what might be a useful mobile app. I would have to say the community seemed…er…underwhelmed with the thought of mobile apps for stuff. But that said, maybe there is a killer app out there waiting to happen. Do you have any ideas on what you’d want to see on a mobile device?

Forum: Bioinformatics Mobile App

Hi Everyone,

We are in the process of creating bioinformatics mobile applications. Rather than common app we want to give app for scholars and scientist for them to access the data wherever they and whenever they want.

Please give your suggestions and recommendations to pick the area or functionalties need to be implemetned.

Thanks.

aeinsights

I thought the discussion was interesting, even if nothing came immediately to mind. Although I recently had some fun with the PDB mobile app, it was mostly to look at cool structures while I was bored in a queue somewhere. I also know that one time at a dinner party the TimeTree app came in handy for looking for a date for a last common ancestor. But I can’t think of much heavy lifting I’d want to do on a small screen. But if you have some ideas, do share them over there.

What’s The Answer? (biggest challenges)

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). Every Thursday 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.

This week’s highlighted question is a pretty broad one. And there’s certainly been discussion of it there, but in addition the original poster used the answers that have been coming along to build a survey. And you have the chance to answer there if you’d like too.

Question: What are the biggest challenges bioinformaticians have with data analysis?

Dear all,

I am doing a research among bioinformaticians, and I am interested in understanding your work, the challenges, and the opportunities.

So my question is, what are the challenges bioinformaticians have with data analysis?

Thank you in advance.

Klemen

So if you are curious about the issues, or have some thoughts, bring them over.

What’s the Answer? (vintage 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). Every Thursday 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.

This week’s highlighted post is actually a BLAST from the past. Although it doesn’t directly say so, it came along around the same time as the “Old Bioinformaticians” conversation. It’s what bioinformatics nerds talk about like your grandparents do, talking about walking to school, in the snow, uphill, both ways–you know? And yeah, I contributed.

But it seems that Pierre Lindenbaum turned this into a curation effort to capture some of this history. I think that’s a nice idea. And people will want these kinds of things for talks and papers sometimes, and possibly for teaching the youngsters. So if you have some of these early bioinformatics artifacts, please contribute them over there.

Forum: Vintage / unconventional pictures for Bioinformatics

I’m looking for Vintage / unconventional pictures for Bioinformatics.

Feel free to add an URL to the picture below. If you’re the owner of the picture, tell me if I you allow me to upload the picture on wikipedia commons.

Please, don’t upvote my answers.

See also: Bioinformatic Cartoon

PS:  e.g: do you have a picture of a printed version of the GCG manual somewhere ?

–Pierre Lindenbaum

Go dust off your items, and share some photos.

What’s the Answer? (openly hate R)

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). Every Thursday 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.

Although I highlighted the original post a couple of weeks back, this Bioinformatics nerd “Uses This” series at Biostar has continued to be really informative and sometimes amusing.  I can’t even extract them to give a fair look because there are so many now, you should just go read them all. Not only is it an interesting cross-section of bioinformatics folks on a bunch of different topics and species, there are really good tips on software tools you might want to know about.

But I’ll extract this piece from today’s chat with Pablo because I used it in the click-baity title:

Forum: Pablo Cingolani of snpEff uses this

What do you use to create plots and charts?
I use R for stats, plots and charts. Although I openly hate R because I think it’s one of the least intuitive programming languages in the planet (followed closely by Malbolge and BrainF***)

Heh. But they aren’t all wonky tools either–some great tips on tools like project management or even remote meeting software have come along:

Forum: Hadley Wickham of ggplot and RStudio uses this

What tools/software do not get enough recognition?
Here’s three that I love and not enough people know about:

  • Selectorgadget: if you ever do any web scraping, you will love the way it learns css/xpath selectors based on positive and negative examples.
  • iDoneThis: we use this at RStudio. It’s a great way to keep track of what you’ve achieved, and to see what your colleagues are working on.
  • appear.in: super simple video chat. No logins, just share a link, and the quality is way better than google hangouts.

Really interesting stuff. Go read “Uses This” posts.

What’s The Answer? (transmembrane protein dbs)

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). Every Thursday 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.

This week’s highlighted question drew less response than I expected. It’s a good question, and would be of major interest for folks looking for druggable targets. So I figured–yeah, there must be a site that focuses on this. But I couldn’t pull one out of my memory banks. I was hoping someone else would. Any thoughts?

Question: Are there any specialist transmembrane protein databases?

I am working almost exclusively with transmembrane proteins. Are there any databases that specialise in categorising transmembrane proteins. For example by membrane type, number of membrane spanning regions, number of non-polar helices, whether the protein is functional or structural, et cetera.

Good Gravy

Bring an answer over there if you know of one.

What’s The Answer? (what do bioinformatics folks use?)

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). Every Thursday 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.

This week’s highlighted item from Biostars is actually one post that was the first of a new series. Inspired by the “Uses This” via The Setup, an interview offers a quick look at what a variety of folks use to do their jobs, Istvan started asking bioinformatics professionals what tools they use for their work. And some other bonus questions.

The first in the series was Jim Robinson of IGV. But since then a number of others have been added (you can follow them with the tag or see the list underneath the first one). Istvan is also welcoming other folks to submit the answers if you want to share what you are up to, and how you get there.

Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this

Based on user suggestion we launch series of posts based on ideas promoted by the Uses This website.

How are the tools that we use every day being developed? What do bioinformaticians with proven track record use to get their work done?

I have sent out a few emails and I will start posting answers as they come in. Feel free to send me candidates (or volunteer) for the interviews.

[The list of questions]

What hardware do you use?

What is your text editor?

What software do you use for your work?

What do you use to create plots and charts?

What do you consider the best language to do bioinformatics with?

What bioinformatics tools/software do not get enough recognition?

[Go over to Biostars to read Jim's answers]

Istvan Albert

Interesting stuff. And more to come. Keep checking.

What’s the Answer? (Reddit bioinformatics AMA)

Usually, we do a highlighted item from Biostar in our “What’s the Answer?” threads to focus on some issues in bioinformatics. But there was an interesting question & answer thread on Reddit Bioinformatics recently that I thought some folks might like to see. For those of you not hip to the reddit lexicon, AMA means “Ask Me Anything”. Reddit is getting more notice and respect for the quality of certain discussions among and with the science community, while, of course, other parts of the place are a complete swamp. I know some women and their allies have chosen not to participate in anything over there because of the bad behaviors that can happen–and I don’t dispute that problem at all. But, sometimes I still find there’s value there.

Bioinformatics PhD with five years in industry. AMA.

Saw the mentoring thread and thought I might be able to answer some questions.

Anyone else with post-school experience? Feel free to chime in.

I thought the discussion was interesting and valuable, especially since we know that academia is increasingly a difficult career path. Go have a look. Add your own insights, too.

What’s the Answer? (domain and lollipop mutation diagrams)

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). Every Thursday 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.

This week’s highlighted question is one that was initially raised a while back, but had new answers recently added so it floated back up to the top. And one of the new answers is a very nifty web-based quick solution that our readers often find particularly handy–I’ll mention it specifically below.

Question: How To Create Mutation Diagram In R Or In Any Tools?

Please let me know any tools or R packages that can create a mutation diagram showing mutations in protein domains like this figure from the MSKCC cBio Cancer Genomic Portal? Thanks in advance

tp53_mutations

henryvuong

There was some chatter about doing some DIY stuff, and some possible R packages that can get there, as well as existing ways to see these at some resource providers. But the new solution that was just added by Jeffk for a web-based easy to use implementation at the cBioPortal is what I wanted to focus on. Their “Mutation Mapper” interface will do the trick, with just a little bit of organizing your data in the right columns. There isn’t a lot of documentation with it, it was just recently released according to the notes. It seems limited to human genes. For other species you can try the other options in the answers. It would be great to see this made more widely available for other species as well.

PS: Other simple web interfaces for domains that we’ve talked about before that remain popular include DomainDraw and MyDomains. You could accomplish diagrams with some of the features with those as well.

Reference:
Gao J., U. Dogrusoz, G. Dresdner, B. Gross, S. O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson & E. Cerami & (2013). Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal, Science Signaling, 6 (269) pl1-pl1. DOI: http://dx.doi.org/10.1126/scisignal.2004088

What’s the Answer? (zero- or one-based coordinate systems)

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). Every Thursday 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.

This week’s highlighted answer isn’t actually found at Biostars itself–but relied on the institutional knowledge at Biostars to assemble this helpful guide. This is a question that comes up so frequently, and burns both novices and seasoned practitioners on a regular basis, that I wanted to make sure people saw this curated information on which tools start with zeros and which ones with ones (er, and those with both….).

I won’t bring the whole post over like I usually do with Biostars, but here’s the link and a snip–go read it all:

Chromosome coordinate systems: 0-based, 1-based

….I’ve tried to figure out which website-application are using each coordinate system. The results can be found bellow. For each source, I provide the URL of the reference website where I found the information, and a caption where the system is described….

Via: