Category Archives: What’s the Answer?

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:

What’s The Answer? (gene essentiality)

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 was a new and interesting question, one I haven’t seen before. Are there resources specifically highlighting essential genes in fly? I can see how a dedicated set of these would be useful, and how it could be challenging to extract that from other, more broad, tools and collections.

Question: database of gene essentiality in Drosophila?

I am looking for annotation of gene essentiality in Drosophila. The ideal resource would be a knockout or a RNAi screening which would tell me, for every gene, whether its deletion or silencing is lethal or not.

I saw that there are many resources online, from flybase to UCSC, but I could not find any annotation on gene essentiality there. There are also a lot of screenings published, but they all seem to be related to specific conditions (e.g. exposure to a DNA damaging factor, stress, etc..), but I could not find any screening in which no special conditions were applied. In general, I not familiar with Drosophila, and I am not sure what an expert in the field would use. Which resource do you recommend me?

–Giovanni M Dall’Olio

Giovanni found a couple of answers and brought them over, but if you know of any other useful collections it would be handy to have that information. I know there are various species knock-out projects, and likely more to come. But I was not familiar with the OGEE (Online GEne Essentiality Database) set. It’s not limited to flies, btw. And as I was reading up on OGEE, I saw a reference in PubMed to another essential gene database that was new to me: DEG, Database of Essential Genes. Reading up on that now too.

References:

Chen W.H., M. J. Lercher & P. Bork (2011). OGEE: an online gene essentiality database, Nucleic Acids Research, 40 (D1) D901-D906. DOI: http://dx.doi.org/10.1093/nar/gkr986

Luo H., Lin Y., Gao F., Zhang C.T. & Zhang R. (2013). DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements., Nucleic acids research, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24243843

What’s The Answer? (elab notebook, open source)

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.

Recently I was watching the genoscenti talk about electronic lab notebooks. I had used the chatter as a post to make a point about the value of the Biostar information on that topic. It seemed to be popular. Lo and behold–there’s a new post on Biostar on this topic. And some nice open-source lab notebook software.

Tool: Introducing eLabFTW : free open source electronic lab notebook

Hello everyone,

I work in Institut Curie, Paris, France, as an engineer in a research lab. I developed a php/mysql application to keep track of experiments (lab notebook). It’s free and open source and I believe this community could be interested in such a thing.

You can run it on a server, for a whole departement if you want, or just locally on your machine.

Please visit the website and try the demo : http://www.elabftw.net https://demo.elabftw.net

Any question, suggestion or remark you might have, I want to read it :) Your input help me makes a better software.

Thank you :D

Regards,

~Nico

elab

The post got a good upvote number, so others found it interesting too. I went to give the software a try, and I thought it was very handy. And Nico was very responsive to my thoughts and working through an idea that I had, as you can see in our exchange. Although I’m not in a wet lab at this point, I really have been musing on the best way to store my thought process and series of steps I’m taking to accomplish certain things I need to do–sometimes in data mining, sometimes in software testing, etc. A system like this could work for my purposes.

Anyway–check it out, eLabFTW. There’s a way to test on a web installation demo that Nico has set up, or you can pull it down locally and run it.

What’s the Answer? (resource gone missing)

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.

So, once again a resource that was published became unavailable. And this had consequences for one researcher–a paper was dinged by reviewers because the resource couldn’t be checked.

Question: What happened with miRecords mirna database website ?

What happened with miRecords mirna database website ? The webpage is not available and I used it’s data as part of an analysis in my paper. Now the reviewer can’t see the page and asks for an explanation.

Edit:

Sorry, I forgot to post the link. The miRecords was suppose to be available at http://miRecords.umn.edu/miRecords.

makaonte

Well, at least the resource is now back up, according to the comments. It was definitely down when I had tried. Apparently writing to the folks on the paper hadn’t succeeded. But is that a win for social media? Or just a temporary appeasement until the next time someone can’t be bothered to restart the server?

Alas. We still need a better way to retire stuff for situations like this.

What’s the Answer? (new Ensembl stuff)

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.

Increasingly, the old method of email announcements of new features is going the way of the dinosaur (but not fast enough for me). Here’s an example of the way to do this kind of outreach now beyond the mailing list–used the “News” category at Biostar.

News: Ensembl 76 is out

We’re pleased to announce that the newest Ensembl release, e76, is out. The new release features:

Read more about our new release on our blog.

Emily_Ensembl

The new Ensembl release has some features you should definitely know about. I love that cell line piece–I went to check it out right away. I’d love to see more resources post their news like that. Anyway–go have a look.

What’s the Answer? (real time collaborative coding)

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 highlight is a new feature from the “Tools” category. I’ve talked about CodersCrowd before–I think it’s a nice teaching tool. But on Biostar the other day I noticed an announcement of a new feature that takes it even further–a way to collaborate on the code in real time.

I’m just going to copy the texty part here, go over and see the example image.

Tool: Real Time Programming for Bioinformatics (and for fun)

Hello all,

I wanted to share the latest development of CodersCrowd with fellow coders here, and let you know that I add a real time programming capability, using the same editor, which is suitable for mentoring, teaching or team oriented coding session.

[big sample image here]

All you have to do is to hit the “collaborate” button when you want to start a new live coding session, and invite your team with the link given to you.

This capability is made possible using the awesome togetherjs from Mozilla

Along with the possibility to run the code using Docker containers this bring a real fun when using CodersCrowd

As always, criticisms are more than useful so dont hesitate, and contributors you’re more than welcome

More about this here http://blog.coderscrowd.com/real-time-programming-for-bioinformatics-and-for-fun/

Rad

There aren’t any comments from folks yet, but it got good up-votes so I hope people are checking it out.