Category Archives: What’s the Answer?

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.

What’s the Answer? (non-PhD bioinformatics job skills)

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 was popular, and offers some chatter on the state of the field with regard to employment opportunities. And this is the kind of question that it’s hard to get answers out of the literature for.

Question: I’m applying for a non-PhD bioinformatics position in your lab. What do you look for?

I’ve been lurking here for years and I’d like to cover a topic that isn’t covered that much.

Bioinformatics is a tough field to not have a PhD. Nonetheless, research positions do exist where only a bachelors is required and research experience is also stated as between 0-2 years. I’d like to give a hypothetical situation that describes a good percent of such applicants to these positions. The motivation here is to survey what are ultimately core requirements for these positions and what is maybe considered “bells and whistles”.

I’m fresh out of college and I have a BS and/or Masters in Bioinformatics along with ~two years research in a lab. I’m applying to your lab, what are you looking for? And what requirement(s) can you excuse or not weight that heavily?

Edit. Sort of a related question, is requiring knowing hadoop and also the biochemistry/biophysics behind RNA-seq at the same time an outrageous expectation for a non-Phd?

scical

Everyone has been following the drama (and the graphs) about how many PhDs vs how many academic jobs there are. Certainly not everyone needs to have a PhD, and this seems a valid and useful question. It got some thoughtful answers from potential employers too. Check out the discussion.

What’s the Answer? (mutation nomenclature)

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.

When I touched on the variation tools at NCBI for this week’s tip, I didn’t go into detail on how the specific variations are designated. But I happened to be looking through the Biostar questions for this week’s highlight, and noticed that someone was not familiar with how the ClinVar mutations are denoted. So I thought maybe others would find that useful information as well.

Question: ClinVar Mutation representations and Descriptions

I was looking into ClinVar data for getting mutation lists. There were mutations which were in the form GENE:c.*** representing they are CDS mutations and GENE:p.*** representing the amino acid changes.

What are those in the following forms represent?

  1. m.***
  2. GENE:n.***
  3. GENE:g.***
  4. nsv***

Example:

TBC1D24:c.1143-6C>T – CDS mutation

NP_002760.1:p.Cys139Ser –  Protein mutation

m.1606G>A ??

U43746.1:n.2241A>G ??

NC_000023.11:g.53254331_53296102dup41772 ??

nsv513787 ??

vigprasud

Have a look at the answers at Biostar. Zhaorong’s answer is correct. This nomenclature is certainly a bit cryptic if you aren’t familiar with the Human Genome Variation Society (HGVS) system. It’s worth looking into the background and framework for this if this is data you are likely to be working with. The history of this strategy goes back quite a ways as you can see from their publication list. But below I’ll add a reference that I think helps to understand the structure if you are new to it.

For even more help in understanding why getting nomenclature right is so crucial–check out the paper below that came out recently, on naming just the TP53 variations . This is a gene that has clinical relevance–and if you are aiming treatments at mutated TP53 you have to be sure you are getting the right one. It’s not just a trivial nuisance to understand how to define mutations–it can matter at the clinic and this will only become increasingly important as we get sequence from more tumors and other clinical situations. And I think this paper makes the point about the complexity and the needs for standardization.

References:
Laros J.F.J., Johan T den Dunnen & Peter E M Taschner (2011). A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form, BMC Bioinformatics, 12 (Suppl 4) S5. DOI: http://dx.doi.org/10.1186/1471-2105-12-s4-s5

Soussi T. & Peter E.M. Taschner (2014). Recommendations for Analyzing and Reporting TP53 Gene Variants in the High-Throughput Sequencing Era , Human Mutation, 35 (6) 766-778. DOI: http://dx.doi.org/10.1002/humu.22561

What’s the Answer? (clinical cancer genomics)

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 sort of pairs with my post from yesterday about the cancer genomics challenge. Despite all the chatter about what will be possible with tumor sequencing, one of the Biostars community members wants to know what we really know, and what we’ve really seen so far on this topic for treating specific individuals. It’s a nice summary type of question that brings together a bunch of the knowledge from folks who are on the front lines and thinking/reading/working on this issue. Biostars works well in this type of chatter, kind of like an international lab meeting.

Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing

What papers are you aware of that attempt the following: (1) Whole genome, exome and/or transcriptome sequencing of (2) live patient tumor samples in an attempt to (3) guide clinical decision making for cancer. The omic events could provide diagnostic, prognostic or treatment response predictions. This approach is widely referred to as personalized medicine, individualized medicine, precision medicine, or precision oncology. There are many reviews describing this idea and many examples that make use of targeted panels (one to hundreds of molecular events). I’m looking for proof-of-principle papers, describing the paradigm where researchers (or tumor genome boards) attempt to use omic NGS data to alter or inform clinical care. These could be N-of-1 case reports or overviews describing experiences with small to large cohorts.

Here is a prototypical example in which an oral adenocarcinoma was sequenced by whole genome and transcriptome sequencing and analysis done to suggest a particular target/pathway for therapy that might not otherwise by considered in this disease type at the time. http://genomebiology.com/content/11/8/R82

[then the post is updated with many examples of the types of papers]

Obi Griffith

In a fast-moving area, with so much literature and/or data getting published in places that might be outside of the PubMed reach at this point, it’s a nice way to collect useful input. Go have a look at the ensuing discussion.