Category Archives: What’s the Answer?

What’s the Answer? (network analysis, plants)

This week’s question comes up on a pretty regular basis, but I always like to see what people are using for exploring the networks of their genes of interest. This was a new species, though, and I was curious to see if there was something particularly relevant to this plant.


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: Network analysis software

I have RNA-seq data for a plant species (Sorghum) that its genome is already mapped, any suggestion for doing network analysis? I prefer to do it without using R packages.

Thanks

mahnazkiani

If you have any other ideas, though, it would be nice to see some suggestions from the plant science side. Go comment over there.

What’s the Answer? (phylogenetic tree tools)

reddit_iconThe previous What’s the Answer? post that we did on something at Reddit Bioinformatics was popular. It led people to some software they weren’t familiar with for editing multiple sequence alignments. So this week we’ll try another post from this subreddit that might be informative for folks interested in phylogenetic tree tools.

reddit question icon Suggestion for phylogenetic tree visualization tools

Hi!
I’m an MS Biology student a bit more on the in silico side of things. One of the projects I’m involved in would require me to visualize (preferably) unrooted phylogenetic trees (based on miRNA sequences). I’m looking for suggestions regarding this problem, what tools should I use?

I’ve used FigTree and UGENE before but I’d like to broaden the palette of available tools.

–submitted by tronke

There were a number of popular tools in the replies: R tools ape, phytools and others, FigTree, Dendroscope, Mesquite, MEGA, and Archaeopteryx. Check out the full discussion thread over there.

What’s The Answer? (proteins without genes in the dbs)

This week’s highlighted discussion offers a peek at some odd situations in public databases. Sometimes there are things missing that you can’t quite figure out. I thought the exploration of why this happens was interesting and informative about working with databases.


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 issue at Biostars is one of the ones that can be really mystifying to encounter. But because of the way databases are curated, sometimes there are odd situations that don’t make sense at first glance. Sometimes these are real bugs–but other times they are decisions that had to be made to accommodate some strange feature of biology that doesn’t align with a database configuration.

Question: Proteins without genes ? Is that even possible ?

Hello all,

I am looking at some mass-spec data.
I found several fragments mapping to Ig heavy chain V-II region WAH protein and want to find corresponding gene.

Example http://www.uniprot.org/uniprot/P01770

Uniprot Screenshot
Uniprot says the gene name as “NULL”. Is this an annotation error or any special aspect of Ig regions am missing ? I want to map several proteins with these type of names to genes.

  • Cluster of Ig heavy chain V-I region HG3
  • Cluster of Ig heavy chain V-II region SESS
  • Cluster of Ig heavy chain V-III region BRO
  • Cluster of Ig lambda chain V-I region NEW
  • Cluster of Ig lambda chain V-II region BUR
  • Ig heavy chain V-II region WAH
  • Ig heavy chain V-III region BUT
  • Ig heavy chain V-III region GAL
  • Ig heavy chain V-III region NIE
  • Ig heavy chain V-III region WEA
  • Ig kappa chain V-I region Kue
  • Ig kappa chain V-I region Wes
  • Ig kappa chain V-III region VG (Fragment)
  • Ig lambda chain V-III region LOI
  • Ig lambda chain V-III region SH
  • Ig lambda chain V-V region DEL

How can I map these to corresponding gene names ?

Thoughts ?

Khader Shameer

Having been involved in curation, I can see how this transpired. But there was a great answer from the UniProt folks themselves in the thread. And input from others too. I thought the discussion was fascinating. Go have a look at the outcome.

 

What’s the Answer? (alignment editors)

PuzzledThis week’s highlighted question is from the Bioinformatics discussion area at Reddit. There are a range of topics discussed in that subreddit, and some of the tool-specific ones are very helpful in learning about new software.

What are some of the best multiple alignment editors that allow for manual editing?

Cross-platform/open-source would be preferred.

AtlasAnimated

There were tools I am familiar with (JalView is the one I have used the most), but I learned about a new tool that looked useful as well. AliView. It sounds as if they have provided a nice tool that manages large datasets better than existing software. As they describe it on their site:

“AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use, not so bloated and hopefully to your liking.”

Heh. Not bloated.

Anyway, looks like it may be worth kicking the tires a bit. In the paper they note that it was related to the 1000 Plants (1kp or OneKP) project “while designing degenerate primers for a diverse set of ferns from transcriptome data”. Anders Larsson talks about the what was needed for this work, and it seems like these needs are going to be common among a lot of folks doing these kinds of large-scale sequencing projects with new species. So I can see this utility of this, and would encourage folks to have a look at AliView.

Quick links:

JalView: http://www.jalview.org/

AliView: http://www.ormbunkar.se/aliview/

Reference:

Larsson A. (2014). AliView: a fast and lightweight alignment viewer and editor for large datasets, Bioinformatics, 30 (22) 3276-3278. DOI: http://dx.doi.org/10.1093/bioinformatics/btu531

What’s The Answer? (what’s next in bioinformatics?)

This week’s highlighted discussion tackles a pretty broad and open-ended issue–what’s next in bioinformatics? The answers varied, interestingly, and presented a lot of great directions. I’d love to see other people’s ideas.


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 is next going to happen in bioinformatics?

In fact many people around the world are working in this domain. some studied bioinformatics and some not (even I see physician are doing bioinformatics). I have been reading papers from all known journals which publish biology related bioinformatics papers or pure bioinformatics. I can tell , pretty much around a topic all times.  I know it is very general question and we cannot give a great and direct answer to it. However, I would like to know which topics you think are the hot spot these days for bioinformatics?

for example, many people are doing sequencing ( of course we cannot have a golden standard because “all modelling are wrong but some are useful “) so these types of studies are going to be forever?

We all know that bioinformatics is only a tool and not the pure science itself. so can we think that it is a died field since mathematics/statistics found itself already or so much left to do ? if so much left to do, what could be those topics ?

I am so eager to know about your opinion

–Mo

I put down some thoughts I had, but I really enjoyed reading the others–like the long one from Francis Ouellette.

What’s The Answer? (beginner projects to pick up)

This week’s highlighted discussion tackles the topic of small projects for folks who are just beginning their training in bioinformatics, or possibly a career transition into a new area. It’s an issue that has come up a number of times, and this new idea for connecting students and projects is a good one, I think.


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.


We’ve talked in the past about having some kind of mechanism to connect students or young coders who need projects with small tasks that need to be done. And just last week one of the searches to our blog brought this: small_projects_bioinfo

So when I saw the discussion at Biostars, I was interested.

Forum: Open Source projects to contribute to

I’m a Computer Scientist/experienced developer looking to get into the field, and contributing to Open Source seems to be one of the first suggestions people make for starting out in bioinformatics.

I was wondering if anyone had any recommendations for open source software projects worth contributing to, particularly ones that might have some low hanging fruit or are in real need of help. Is there any tools you folk are using right now that really needs feature X or are you a project maintainer that needs a dig out? The difficulty I’m having is that because I’m not working with these tools day to day, I don’t have the best view of the commonly used tools and their associated problems.

So if anyone has any suggestions I’m going to try fit in some OSS contributions with my own contracting jobs/spare time bio studying. My programming background is Java, Javascript, Python, PHP and I’m learning some R at the moment while I do some coursera specialisations. I’ve done quite a bit of systems admin if the work involved server-side clustering/distributed systems etc.

Thanks

–shane

The answer with the idea for the “Pick me up!” tag struck me as a good system for this sort of thing. Maybe others could implement this kind of tag on their projects too, if they have suitable small tasks. So I thought I’d raise the awareness of that a little bit–in case someone comes to us on a search for “small academic projects in bioinformatics” again. I hope they find some. I still think it’s a need on both sides.

What’s The Answer? (Internet of DNA)

This week’s highlighted discussion tackles the “Internet of DNA”, a story I picked last week in my SNPpets post, which has bubbled up elsewhere. And Biostar folks look at the more technical implications of “A global network of millions of genomes….”


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 discussion comes as part of an interesting week on the personalized medicine front. A whole bunch of things are coming together–the US getting a Chief Data Scientist who talks about bioinformatics, The NEJM talking about training physicians to deal with medical genomics issues, and the “Internet of DNA” getting out into the popular science media realm. So have a look at what bioinformatics nerds made of this, and what their thoughts are:

Forum: A global network of millions of genomes could be medicine’s next great advance. | Beacon

Internet of DNA

A global network of millions of genomes could be medicine’s next great advance.

Availability: 1-2 years

Noah is a six-year-old suffering from a disorder without a name. This year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world like him.

http://www.technologyreview.com/featuredstory/535016/internet-of-dna/

Do you think this will happen within 2 years?

Edit:

This is the technical implementation I think  that they are talking about:

The Beacon project is a project to test the willingness of international sites to share genetic data in the simplest of all technical contexts. It is defined as a simple public web service that any institution can implement as a service. The service is designed merely to accept a query of the form “Do you have any genomes with an ‘A’ at position 100,735 on chromosome 3″ (or similar data) and responds with one of “Yes” or “No.” A site offering this service is called a “beacon”.

http://ga4gh.org/#/beacon

So it just a federated query over multiple large genomics (+ phenotypes) data sets. Full genomes are not centralized, or moved, so privacy is less of a concern.

William

And please, contribute your own thoughts over there. We need to be having this discussion. Also, watch for more on this Beacon….

What’s the Answer? (RStudio as a game-changer)

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 part of the week’s them on statistical computing. The post comes from someone who is a biologist, is remembering what it was like before we had the nice RStudio interface. And he offers some hand-holding to get new users started.

Tutorial: Few words for R beginners

Hi,

As a biologist who started to learn R, I encountered a lot of problems on learning the subject. Now I don’t want to go into them but I just want to suggest what I think that can save you from wasting your time and energy fooling around without getting what you expect.

  1. Install R ! Of course!
  2. Install R-studio, this simplifies your life. Note: R-studio should be installed after R. (http://www.rstudio.com/). After this you always open R-studio not R. R is the actual program but R-studio gives it the nice interactive interface.
  3. Watch this webinar on R to get familiar with basics and why it’s good to have R-studio. http://bitesizebio.com/webinar/20600/beginners-introduction-to-r-statistical-software/
  4. Coursera offers this very nice course in R. Get the videos from their website and of course watch them! (https://www.coursera.org/course/rprog)
  5. While learning from the course, practice with swirl ( http://www.swirlstats.com ). Swirl was the best R teacher for me. It interactively makes you work around with R.
  6. Also https://www.datacamp.com/courses/introduction-to-r or generally https://www.datacamp.com is very good resource for self learners!
  7. Stuar51XT is a youtube channel that has very nice comprehensive R courses. Just in their videos search for “introduction to R programming” https://www.youtube.com/user/Stuar51XT .
  8. Practice and expand bioinformatics oriented R skills by “Institute for Integrative Genome Biology” manual. http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual

If I go back to my pre-R era I would follow the above. I think its a good kick-off for those who want to learn R and start getting familiar with R’s environment.  I hope it helps you =)

Cheers!

–Parham

But I also loved this response:

I would add, as someone who started using R around 13 years ago: RStudio has been a complete game-changer. It has made the software far more accessible to more people, brought together a great combination of developers, been responsible for many useful, innovative packages and all-in-all, is just A Good Thing.            – Neilfws

See, it’s not just me trying to lure you to RStudio. It is A Good Thing. There are some other comments over there too with more tips or chatter. Go have a look.

 

What’s the Answer? (wet lab software)

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 about some wet lab software. Typically we are looking at genomics analysis tools, but with the high-throughput nature of current biology it seems to me there’s good opportunity for more of this type of resource management software too. And the software developer is looking for some feedback from other types of researchers.

Tool: StrainControl Laboratory Manager software

Dear all,

I have read some posts regarding lab software’s, so I thought that maybe ours could be of interest.

We that have developed the software, StrainControl Laboratory Manager, all work in the field of science.

Last year StrainControl was released to the research community.

StrainControl is a lab software that allows to you to store everything in the lab in one place.
Currently there are about 700 labs that are using StrainControl and they are all satisfied.

Some key functions:
1) Handle strains, cell-lines, oligos, plasmids, chemicals and inventories.
2) Link plasmid data to strains or cell-lines.
3) Ability to rename any field and text to your own needs.
4) Customize which data columns should be visible.
5) User management allowing you to create read, write, administrator accounts etc.
6) Read-access from cloud drive (dropbox etc) and network support.
7) Create reports (over 20 formats)

What I´m interested in is if any other research fields (beside basic research labs) can make any use of the software since any field can be renamed to fit a different research field.

We would be very happy if you could give it a try and comment how the software works for you.

More information: http://www.straincontrol.com

Thank you in advance,
Chris Ericsson, PhD

And some of our most popular blog posts are about colony management software, electronic lab notebooks, and other sorts of routine stuff–not just analysis tools. So have a look and see if this is useful. Or if you have other tools like that which you find essential to lab work, let  me know. I’d love to have a look.

What’s the Answer? (free images for science communications)

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 isn’t about the usual topics–software or tools for genomics per se. Someone recently asked about accessing free images for papers, and this is also something I need for presentations. I mean, I know this isn’t directly related to genomics necessarily–but communicating is pretty useful too. And pretty common in science….

Question: Images — Free common images for articles?

Hello!
I’d like to ask You — is there any open database for downloading free (totally newbish) images such as “DNA structure”, “protein synthesis” and so for placing them into article? NCBI used to have image search which now refuses to find these basic images. Am i doing something wrong or is there any other place for such images?

Thank You very much in advance

ldpubsec

And the mechanism for finding the rights at Google was new to me. I thought maybe it would be new to others as well. Go see. I’ve also added a couple of other sources that I use, I think people would find them handy–such as NHGRI and NIH images.