Category Archives: What’s the Answer?

Biostars

What’s the Answer? (genomics guidance for the general public)

This week’s highlighted discussion at Biostars was one that I opened. I’ve been thinking a lot about this, because I’m seeing it come up in a number of different ways. There are folks who are googling and finding genomics nerds in a variety of places. Some of the communities will be more welcoming than others. But I think it’s in our best interest to be helpful to families with data, and not come off too harsh because it’s not exactly how our forum works….


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.


Forum: For the general public seeking advice from this community

Hello folks–

Yesterday I saw a thread posted by a member of the general public, looking for advice for their child’s medical issues. This thread has been deleted (I think), but I was able to read some of the commentary before it disappeared.

The community had some concerns about private medical information being revealed. And some concerns about seeking advice from strangers on the internet instead of qualified practitioners in real life. These are valid issues.

However, my point is more general. This may become increasingly an issue here as more people have (or hear about) sequence information, and want some advice for it. I think it is wise for this community to stay away from diagnosis. But I think we could offer these folks some guidance to appropriate resources.

Please have some compassion for the desperation that the parents of kids with undiagnosed conditions face. And keep in mind that their thresholds for privacy are not the same as everyone else, possibly. And understand that they are hearing stories about how familes connected with researchers who could help them from random internet forums. The most recent one I saw was this: Answers.

But other stories like this are widely read: How Genome Sequencing Creates Communities Around Rare Disorders.

Could we possibly have a place to point these families, like a thread that we can sticky or something? Where we can offer them connections to the Rare Disease sequencing projects, or genetic counseling resources, non-wonky information sources like Genetics Home Reference, or something? The international group here probably could collect a good set of pointers for people around the world.

I guess I’m asking for a constructive place for some guidance for families, and a policy about how to deal with those kinds of threads.

Open for discussion.

Has any of the genomics nerd discussion communities developed a policy on this? Should we reach out to genetic counselors, maybe? We may also need legal advice. Anyone seen other places take this on? Please add your thoughts over at Biostars.

Biostars

What’s the Answer? (visualize genomic rearrangements)

This week’s highlighted question at Biostars is a helpful summary of a number of tools available to solve this visualization problem. Although phrased in the form of a question, the original poster was actually providing a helpful list of the ones he’s investigated already, but he also wanted to know what was availble that others might be using. So it had content and generated some nice discussion on the subject as well.


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: Which program, tool, or strategy do you use to visualize genomic rearrangements?

In relation to my master thesis I’m working on tools to visualize fusion genes. In that regard I’m interested in any and all strategies and tools that exists for visualizing genomic rearrangements. I’ll include the list I have so far below, and update the list when I get answers.

Programming packages:

  • Circos: Perl package for circular plots, which are well suited for genomic rearrangements.
  • J-Circos is a java application for doing interactive work with circos plots.
  • ClicO FS: an interactive web-based service of Circos.
  • rCircos: R package for circular plots.
  • OmicCircos: R package for circular plots for omics data.
  • ggbio: R package for visualizing biological data. Has a circular view similar to the previous packages.
  • D3 chord diagrams (javascript) can be used to visualize genomic rearrangements. See this plot of migration flows as a similar example.

“Complete” tools:

[there's a series of images with examples here, I don't want to paste them all--go have a look]

stianlagstad

There were a number of additional tools listed in the comments. You should go over and look. And if you have other ones that are not yet over there, help a student out and add them.

Biostars

What’s the Answer? (building the ultimate bioinformatics resource)

This week’s highlighted item will apparently answer all the questions in the future, rendering my weekly foray moot. Ok, kidding aside, I think this is a great idea. A sort of “living” better-than-textbook project that will really be the only way to keep up with a field that changes as fast as bioinformatics does. If they can pull it off.


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.


I have been teaching bioinformatics courses for a few years now and I have always felt that existing resources were inadequate.

Most are either too programming and unix oriented or too focused on one particular “protocol” ignoring alternatives that may produce different results. In addition most resources tend to focus on installation and running the tool rather than understanding the outputs. Disclaimer: I am guilty of this as well! I always felt that I had to start from zero each time I write a guide and towards the end there is too much material already and I have to cut short at the most interesting parts. But that is because there has never been an updated and reliable resource that I can refer people to. Until now. Biostar_handbook

I am starting a “bioinformatics handbook” resource it is called the Biostar Handbook. I would like it be a repository of practical advice on bioinformatics methods, a resource that is useful to both beginners and advanced users, a collection of curated experiences of bioinformaticians around the world. The book will be comprehensive with ebook and online components that will continue to grow and expand over the years. It will come at very low cost of about $25 to ensure that the task of maintaining, correcting and supporting it won’t solely require personal enthusiasm and could be contracted out if necessary.

I would like to invite everyone to contribute via GitHub: you will retain authorship, copyright and distribution rights on all content you create. And since we are creating the ultimate guide to Bioinformatics ;-) I think it will be great adventure for everyone involved.

Contribution guide:

http://biostarhandbook.com/contribute.html

Book website:

https://leanpub.com/biostarhandbook

Help us create the best bioinformatics resource that was ever conceived!

Istvan Albert 

Traditional publishing is out of date in so many ways. But in a field that changes so quickly, there has to be another solution. The initial design and idea for Biostar was to be an active question and answer resource with up-to-date information about bioinformatics tools and strategies. Evolving it into a more cohesive teaching resource is a neat idea. This has to happen. And I hope it flies. Check out the discussion at Biostar to see how it’s being received. And over at the book page you can sign up to be notified about the availability. Do sign up to show some support for the project if you are interested. And/or, contribute your own important chapter!

Reference:

Parnell, L., Lindenbaum, P., Shameer, K., Dall’Olio, G., Swan, D., Jensen, L., Cockell, S., Pedersen, B., Mangan, M., Miller, C., & Albert, I. (2011). BioStar: An Online Question & Answer Resource for the Bioinformatics Community PLoS Computational Biology, 7 (10) DOI: 10.1371/journal.pcbi.1002216

Biostars

What’s the Answer? (cancer data visualization tools)

This week’s highlighted question was less of a question than a notice about a new tool. And because I’m always interested in exploring new visualization tools, I was interested to have a look. In addition, we are frequently asked about tools specific for cancer genomics, and I like to be able to tell people about what I’ve found.


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 (well, the question mark was edited out later, but this is what it said when I grabbed it):

Tool: A new tool for cancer researcher developed by UCSC?

Another tool XENA that comes to the world of Bioinforamatics designed by UCSC. I am not sure if people are aware of it. It is developed recently and I got the notification last evening. Seems to be having a lot of potential for both data visualization and also producing quality images for publication. The paper is not yet out but the mention of the tool was done last year when the update paper of the UCSC Cancer Genomics browser was made for 2015.

The tool has got data from both TCGA and ICGC and is a powerful resource not only for public data comparing and viewing but also one can upload its own data or download the tool locally to a desktop app version and visualize it. The tool is available at the below link

http://xena.ucsc.edu/

The technical doc is here . Am sure it will be a great resource for the researchers and bioinformaticians across the globe. For analysis it also integrates the galaxy as well and if you format your data in a version as mentioned in help docs one can view their data as well. Enjoy and appreciate the work. Hope people would like it.

P.S:

I am not involved in the work. I liked the tool a lot so thought of informing it to the community

vchris_ngs

It also generated a bit of discussion about the challenges of developing visualizations. Go have a look.

reddit_icon

What’s the Answer? (novel pathways in silico)

reddit_iconThis week’s highlighted discussion is a different take on pathway and network tools. This is about the design of novel metabolic pathways in silico, not just exploring existing pathways to look for where your favorite genes play roles.

reddit question iconIs there free software available for designing metabolic pathways? (self.bioinformatics)

submitted  by learnedidiot

I am interested in designing novel metabolic pathways in silico, and was curious if there is a good software packages that allows for finding the shortest path in terms of enzymes, regardless of species, for a given input to final output?

Although we have talked about COPASI before, in conjuction with GenoCAD, and we’ve done training on STRING, some of the other tools were new to me and I was pleased to learn of them. If you know of others you can offer the suggestions. Go have a look at the discussion.

reddit_icon

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.

reddit_icon

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.

reddit_icon

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.

reddit question icon

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.