Category Archives: What’s the Answer?

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.

What’s The Answer? (SNPs in promoters)

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 I hear a lot in workshops.

Question: Database for finding SNPs (Mutation-deletion/SNPs) In the promotor region of any gene

Is there any online database in which I can find the mutations in the promotor region of oncogenes. Cosmic and other databases are not good for that purpose.Any one ???

vrun.bnsl

The only answer over there has several nice options–go have a look.  We’ve talked about some of them, but I should really think about doing tips-of-the-week on at least one of them. Stay tuned.

What’s the Answer? (electronic lab notebooks)

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 actually started on Twitter, and led me back to Biostar. I saw this question come across:

And I was interested in several of the answers. But one of the great things was the answer from Pierre–links to Biostar–with several different discussions of this.

This is a resource with history and depth! And although those answers were some time ago, they offer useful thoughts about the features to consider when making a choice. So that kind of institutional memory can be really helpful.

But I was also interested in the other answers–including DokuWiki, “universal open-source Electronic Laboratory Notebook” (referenced below), Labguru, and other people’s less formal solutions and suggestions.

Reference:

Voegele C., N. Robinot, J. McKay, P. Damiecki & L. Alteyrac (2013). A universal open-source Electronic Laboratory Notebook, Bioinformatics, 29 (13) 1710-1712. DOI: http://dx.doi.org/10.1093/bioinformatics/btt253

What’s the Answer? (free + useful protein tools)

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.

One of the things we still don’t really have a handle on is the “lists of tools” problem. I think this leads to some really unfortunate duplication of efforts. A lot of folks have attempted to create lists of tools for certain purposes, but they are hard to maintain, the focus of the lists vary. Sometimes useful tools are found in unusual or informal places, sometimes hard to categorize, and the support…well…yeah. So I keep tabs on various lists that I find, because sometimes there are some gems in there which are new to me. And to have active practitioners describing what’s useful to them is particularly helpful.

This week’s highlighted post is from someone focusing on protein tools, who is collecting a list of them.

Tool: A growing collection of “Free and useful protein-science tools”

I thought that it might be useful to put together a list of the tools that I am currently using with a short description and usage example.

I will add to it in future, and I am also looking forward to contributions: Please feel free to add your favorite tools if you like:

https://github.com/rasbt/protein-science/blob/master/scripts-and-tools/more_protein-science_tools.md

se.raschka

Check out the current list, and suggest others if you have some.

What’s The Answer? (data sharing with Bittorrent)

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 item is a new feature–and they are looking for your input and testing if it is a feature you might use.

Forum: Data sharing via Bittorrent is coming to Biostar

Hello Everyone,

We are adding bittorrent data sharing to Biostars.  Help us identify bugs and issues by creating a few torrents and adding them to posts on the test site. Also feel free to comment and provide suggestions and feedback. The description of how it works is at:

http://test.biostars.org/info/data/

An example post with data can be seen at:

http://test.biostars.org/p/101/

A few details on how it works:

  1. Torrents can get attached to posts, answers or comments
  2. A post may have multiple torrents attached.
  3. Biostars will attempt to connect the IP number of the Bittorrent peer connection to the IP number of the Biostar user account. This allows you to see who the person that shares the data is.
  4. Anonymous users cannot create torrents but they may share existing datasets.
  5. Data may be shared without making it visible on Biostar (although this should not be considered a secure way to share data)

(note: the test site will not log you into your old account since the emails are protected so don’t report that as an issue)

Istvan Albert

Although it seems to be well received, people have issues with some institutions that don’t allow Bittorrent access due to some past bad behaviors…so people have raised that issue. So if you want to try it out, or have concerns, let ‘em know over there.