Category Archives: What’s the Answer?

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What’s the Answer? (expression across tissues)

reddit_iconThis week’s highlighted question is one that I like to look in on from time-to-time, to see how people are solving the issue of looking at tissue expression. In this case none of the tools were new to me, but I do like to see what people prefer. And I like to spur some discussion if other folks have tools that aren’t already described, or newer ones that I jut might not have come across yet.

So have a look at this question and thread. If you have other suggestions, chime in.

reddit question icon

Expression levels across tissues? (self.bioinformatics)

submitted  by Wunterslash

Does anyone know the best databases or methods of exploring gene and/or protein expression levels across different human tissues?

I was pleased to see that one of my favorites for this issue was included already, so I didn’t chime in. BioGPS. Of course, BioGPS does more than just expression–I have always liked the way you can pull in the annotation types you need. But I just happened to like this way to look at expression data.

But go have a look at all the answers. Add more if you have suggestions.

Biostars

What’s The Answer? (consumer genomics help)

This week’s highlighted questions are part of a larger “meta” thing that I keep musing about. Recently, independently, these questions showed up at the Biostar site.  Interesting convergence of questions from the public, I thought. Although some folks wading into recreational genomics have some biology or computational background, so many of the ones coming from genealogy or from a family’s eager adoption of testing all the relatives of this may not. They probably don’t know what a reference genome is. They won’t get the plug-in idea. They don’t know what the right questions are. I think this is just the tip of an iceberg.


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.


Question: Reverse gene lookup from SNP

I’ve exported my 23andme results, and the resulting spreadsheet contains only the rs# and genotype. I would also like an extra column that lists the genes that these particular SNP’s belong to where applicable.

I realize it’s easy to find rs#s given a gene, but how do you find a gene that an rs# belongs to, if indeed it does belong to a gene? Is there an automated way to do this? Thanks.

mass2

And:

Question: Is it possible to load export files from AncestryDNA into IGB?

See title. There’s not a lot more than that to say :) Thanks.

drmoose94

People are wanting help getting their consumer data into the tools. These are probably more advanced consumers, but more and more this will become an issue. And I hadn’t seen the tool providers doing support or outreach for that until I saw this answer from Nowlan at IGB.

One of the optional plug-ins for IGB converts raw 23andMe SNP data into a BED file for viewing. AncestryDNA data is quite similar to 23andMe data, so we could add a new plug-in to convert AncestryDNA as well.

I can imagine there’s some hesitation, lest people make some bad conclusions from some possible interpretations. But there’s also opportunity here to get people interested in genomics in new ways. But the level of support they need is very different. Their questions are coming, though. Just yesterday this was in the searches to this blog:

23andme_question

I’ve seen this kind of thing before, too, and I assume all genomics bloggers are seeing stuff like that. I keep thinking someone will do some kind of consumer browser, too, and I’m still not seeing that. I really think it’s time now. I continue to dream of genomics outreach that is like “extension” services that agricultural schools in the US have. Their mission is to roll out appropriate tech and info to the practitioners–farmers and the public. I wish the Precision Medicine initiatives had something like that. But I haven’t seen any talk of it.

Biostars

What’s The Answer? (down for everyone, or just me)

This week’s highlighted question was useful in a couple of ways. First, it offered a way to check if a site is down just for you due to local connection issues, or if it appears down for everyone. I used one of the suggested sites before, but I wasn’t aware of the other one. So that was handy. But I also thought maybe readers aren’t aware of these tools, so I figured I’d spread the word on that.

But it also led to a broader discussion of pathway and annotation tools. I know people are increasingly frustrated with DAVID, but it’s still widely used. So there were also some suggestions for other tools for similar types of analyses, and a couple of them were things I’ll be looking at further.


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.


So here’s this week’s highlighted question:

Question: DAVID pathway analysis

Hi,

First time posting so apologies if this is posted to the wrong forum.

Does anybody know if there is an issue with the DAVID website. I’ve tried accessing it from several computers but it won’t load. I could get in last week but when using the conversion tool it would stop at 30% complete. I’ve tried emailing them but have not got a reply.

Thanks,

Alan

yourell.alan

Check out the answers on this helpful thread.

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What’s the Answer? (101 Buffalo questions)

Bet that made you look. This week’s question post is about someone else’s question post. It’s so meta. I happened to see it in Reddit Bioinformatics this week, but I’m sure it will make the rounds of other social media too.

reddit_article_button

101 questions with a bioinformatician #30: Vince Buffalo (acgt.me)

submitted an hour ago by kbradnam

[-] kbradnam [S]
I mostly refrain from linking to my ACGT blog on reddit, but I feel that Vince Buffalo is going to be a bioinformatics star of the future a bioinformatics book published while still in Grad school!), and wanted to share this one particular interview.

I don’t usually post further reddit comments in full, but you’ll see why I’m including this one. I have bought this book, in an early version. I would recommend it too.

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What’s the Answer? (NGS tools you are using the most)

reddit_iconThere are a lot of tools in the bioinformatics ecosystem. Some of them you won’t ever need because of your particular research focus.  For some of them you may want to know about similar alternatives. But my favorite types of discussions with practitioners of various sorts is what are they actually using. This week’s highlighted question asks that of folks working with NGS data.

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Those working with NGS data – what is your list of most used tools?

submitted  by lc929

Command line, Galaxy browser? Sam tools? Thanks.

It’s really great to know what’s actually in use and working for people. Go have a look at the answers. Contribute some thoughts over there as well if you have favorites.

Biostars

What’s the Answer? (rewarding good coding behavior)

This was a nice twist on the usual complaints about code and documentation. A way to recognize good behavior and illustrate examples that are well done. I liked it.


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.


Forum: What are your “model” examples for bioinformatics programming?

We’ve talked a lot about Minimum Standards For Bioinformatics Command Line Tools here, but I’m wondering what you consider to be “gold standard” examples of coding/programming that bioinformaticians should read to improve their own coding and understanding.

I’ll start:

Picard – written in Java

Sickle – written in C++

Cutadapt – written in Python

Dan D

Anyway, I thought it was a good idea to show the kind of behavior you want to encourage. Check out the chatter and add other good examples, if you have some.

 

What’s the Answer? (which genetic code)

This week’s highlighted question is a kind of a basic one, but as more and more sequence data comes along from species that people might not have worked with before, it’s kind of a handy tip to keep in your back pocket.


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.


Question: Database that says what genetic code a particular organism uses?

I’m at ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt with all the genetic codes.  Trying to figure out what genetic code Nostoc punctiforme uses.  Is there a database that has which version they use? I know it’s not standard and they have multiple start codons.

jolespin

The very helpful response from h.mon described where to find it on the NCBI Taxonomy pages and the link to the details. Go click through.

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What’s the Answer? (treasure hunt)

reddit_iconThis week’s highlighted question is from the Bioinformatics subreddit. I thought it was a neat idea–something that totally would have engaged me as an undergrad in the summer with time on my hands. So I thought I’d help out with some promotion for this treasure hunt.

reddit question icon How to promote a bioinformatics themed treasure hunt?

I recently released Excision, an adventure and treasure hunt that takes players through a series of introductory computer and bioinformatics puzzles. Players go through the game as a brand new Agent in a near-future society. There’s even a $50 prize for the first person to make it through all the stages.

I’ve gotten some pretty positive feedback from those who have played, but I don’t know anything about marketing and haven’t done a great job of promoting Excision. If anyone has any suggestions on how I might go about getting more visibility, I’d love to hear any ideas.

And, of course, here’s the link for anyone who wants to check it out for themselves!

http://what-is-bioinformatics.blogspot.com/2015/02/base-camp.html

LifeIsBio

Might be a fun teaching tool for some folks too. Isn’t it what we are all doing, hunting for treasures in the genomes? Anyway, I thought it was a cute concept. Check it out.

Biostars

What’s The Answer? (effective altruists in bioinformatics)

As this week’s lighter holiday fare continues, here’s an interesting and unusual question about career directions related to bioinformatics. I’d love to see how this comes out 10 years from now.


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.


Forum: A Bioinformatics Career for an Effective Altruist?

Hi.

My situation:
- Living in Portugal. But I have no problems in going to other countries.
- Just finishing my Biology’s Bachelor’s Degree
- Know some Haskell and Matlab
- I’m doing the The Odin Project course (http://theodinproject.com/curriculum). I already know some HTML, some CSS, some Ruby on Rails and a good bit of Rails, I think.

What I Want
- I want to be a Effective Altruist (https://en.wikipedia.org/wiki/Effective_altruism), that is, I want to do the most good possible in the world. I could have a very-well-paid job and give a good percentage of it to charity (a strategy called ‘earning to give’). Or I could have a job with a direct impact on people, like biomedicine research on important problems. Or I could mix the two strategies.

Problem

I’m thinking about getting a Masters on Bioinformatics. But I’m afraid that after finishing it I could get a not-very-well-paid-job compared with other informatics-related jobs and that that job would not have a great positive impact on society. Maybe what I would give to charity with the earnings from other informatics-related job would do more good in the world.

On the other hand, I have no formal education on informatics.Could I really get a well-paid job in the area just from self-learning?

Questions

- How much positive impact does bioinformatics research has on the world?
- How a bioinformatics master’s degree would raise my chances of one day have a really-well-paid-job compared with just self-learning?

Thanks. :D

Luís Campos

Ps: There’s a worldwide community of effective altruists, so I think the answers to this question have the potential to have a high impact on some person’s carrers

–luis1212

I enjoyed reading people’s thoughts on this, and added one of my own.

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What’s the Answer? (subreddit r/genome)

reddit_iconSome researchers who currently enjoy (or at least tolerate) twitter are concerned about its ongoing support, stability, and effectiveness. Some of them are now adding a reddit section to their social media options. I noted this in our Friday SNPpets, but thought I’d also show you a concrete example of how it’s being used.

Reddit version:

Kaiser Permanente cohort of ~100k individuals with genotypes and phenotypes
submitted by josephpickrell

Kaiser Permanente (an insurance company in California) genotyped around 100,000 people [edit: I should note this was in collaboration with UCSF], and made the data available on dbGAP.

Today I noticed three papers describing aspects of the data:

  1. A description of the genotyping and quality control
  2. A comparison of genetic ancestry to self-reported race/ethnicity in the cohort.
  3. A description of a telomere length assay on all individuals.

My personal experience is that these data are well-organized and accessible, so it’s great to see more details on how they were collected. I’ve only seen a few papers that use the data, for example Loh et al. used the data to calculate genetic correlations between several of the phenotypes.

There was the release of some information that might be helpful to researchers. And instead of a fleeting notice on twitter, this post in the subreddit is available at any time. You can also discuss it in longer form, include more links, and your timing doesn’t matter. I can see the value of this. But I know some people aren’t crazy about Reddit. We’ll see how it develops. So far, though, seems popular.

Visit: https://www.reddit.com/r/genome/