Video Tip of the Week: Atlas of Cancer Signaling Networks

Last week I highlighted a software tool that lets you customize maps of molecular interactions, and navigate around at various resolutions to explore. It’s called NaviCell, and it seems to offer a lot of opportunity for folks to develop helpful maps related to their research. This week I’m going to note that this same team has created a collection of maps for cancer signalling, based on the NaviCell framework.

The Atlas of Cancer Signaling Networks demonstrates how you can create a collection of interaction maps that will be useful for a particular research focus. Using the same basic features described for NaviCell, you can create and explore data sets with a Google Map foundation and interactivity.

I won’t go in to any more detail on the map use and creation guidance that I covered last week, you can click over for more. But if you liked NaviCell, ACSN should give you a great sense of how to implement this for your own research topics of interest as well.

Quick links:

Atlas of Cancer Signaling Networks: http://acsn.curie.fr

NaviCell: http://navicell.curie.fr/

References:

Kuperstein I., Cohen D.P., Pook S., Viara E., Calzone L., Barillot E. & Zinovyev A. (2013). NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Systems Biology, 7 (1) 100. DOI:

What’s The Answer? (GMOD resources training)

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.

I’m going to run this post on Tuesday this week rather than Thursday because this has a deadline that you need to hit if you want to sign up for this and I want you to have a couple more days. And I spend much of Thursday on a plane on my way to do workshops anyway….

Are you interested in an online 5-day course in using the awesome GMOD resources for analyzing, organizing, and displaying your data? In the News area at Biostars I posted this announcement that you should check out.

News: GMOD Online Training 2014 coming up

GMOD Online Training

http://gmod.org/wiki/GMOD_Online_Training_2014

19th-23rd May 2014, approx 9am-6pm US Eastern time

The Generic Model Organism Database (GMOD) project is offering an online training course for those interested in learning how to use and deploy GMOD’s free, open-source bioinformatics software. The GMOD project provides interoperable tools for visualising, storing, and disseminating genetic and genomic data.

The course will be held from 19th-23rd May 2014, with tuition and interaction with tutors occurring between (approximately) 9am and 6pm US Eastern time.

[go over to Biostars to see the list of topics covered and for more details]

–Mary

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

What’s the Answer? (new Biostars interface)

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.

Ok, it’s not so much a question this week, but a heads-up. There have been some changes over at Biostars that you should be aware of. If you haven’t logged in for a while, it can be interesting.

Here’s the post about the new interface, and some details about the status of some features.

Forum: Biostar 2.0 released, by Istvan Albert

Biostar 2.0 is now live.

This is the result of quite a few months of work and we hope to have added valuable improvements. We may have bugs and display oddities so please bear with us while we identify and fix them.

The overarching theme is that of providing better search and  navigation and improved tracking of existing content.

[lots more details over at the post]

There’s another post about someone who logged in but seemed to have a different account, causing some confusion, so just be aware of that aspect. But if you have trouble you can see the release post for how to get help.

When I first logged in to the new setup I was greeted with many cheery badges having been awarded, and new notifications that weren’t really new notifications. But they made me smile, anyway! Biostar_appreciated

I feel appreciated.

Anyway, check out the new look: Biostars.

If you are new to Biostar, and not a regular reader, there’s more background on the philosophy of the site in this paper:

Parnell L.D., Lindenbaum P., Shameer K., Dall’Olio G.M., Swan D.C., Jensen L.J., Cockell S.J., Pedersen B.S., Mangan M.E. & Miller C.A. & (2011). BioStar: An Online Question & Answer Resource for the Bioinformatics Community, PLoS Computational Biology, 7 (10) e1002216. DOI:

Video Tip of the Week: NaviCell for custom interaction maps for systems biology

The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a tool that aims to help standardize and represent the key features of they systems biology and molecular interactions that we need to capture.

NaviCell came to my attention as I was watching the tweets from the recent #isb2014 conference: The International Society for Biocuration conference. Suddenly a bunch of excited attendees started chatting about it:

So I went to investigate. And I can see why they liked it. This excerpt from the abstract of their paper (linked below) captures the key aspects very nicely:

NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback.

So you can use this web-based interface to create, curate, and navigate around molecular interaction diagrams in a really useful way. I haven’t seen any video of this talk, but they do have a video that offers an overview of their tools.

They have maps available to get you started exploring the tools and features. You should also access their documentation. They have separate guides for general use and for creating and uploading your own maps. Their literature section also has a good collection of papers that will help you understand the context of their tool in the ecosystem of pathway and interaction data–but you can also read their paper for a nice description of it all. The standards efforts are important to grasp, and you’ll also need CellDesigner (which we covered in the past) to create your own maps.

Quick links:

Navicell homepage: http://navicell.curie.fr

CellDesigner: http://celldesigner.org

References:

Kuperstein I., Cohen D.P., Pook S., Viara E., Calzone L., Barillot E. & Zinovyev A. (2013). NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Systems Biology, 7 (1) 100. DOI:

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N. & Kitano H. (2008). CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, 96 (8) 1254-1265. DOI:

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

 

 

What’s The Answer? (1000 Genomes signatures)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar 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 BioStar.

In addition to the discussion and question sections, Biostar also has a section that allows contributors to publicize their tools and workshops and stuff like that. It’s called “ads” but don’t let the make you squeamish. I don’t think I’ve seen anything for sale–it’s been used to merely highlight the availability of some database or training so far. Outreach to scientists is tricking–it can be perceived as icky, but we really need ways to tell people about the tools out there.

I’ve been meaning to mention this tool but some other topical things had come up in the meantime. But now I wanted to mention this. It’s a custom installation of a UCSC Genome Browser framework that offers new ways to look at variations from the 1000 Genomes project.

Ad: A database of Signatures of Selection in the 1000 Genomes dataset

The 1000 Genomes Selection Browser is a database of Signatures of Selection in the Human Genome, based on the 1000 Genomes Phase I data. It is freely accessible at http://hsb.upf.edu/

The browser, based on a custom UCSC Genome Browser installment, allows to easily navigate the genome and visualize regions that are candidate for having been involved in an event of selection in any of the African, European, or Asian populations. The data can also be easily downloaded for further analysis here.

Our browser includes a total of 17 tests for selection. For each test of selection, we provide a raw score, plus a ranked score which compares each position to the rest of the genome.

[long list of the tests with further details....]

Go have a look at the details and then go over to the 1000 Genomes Selection Browser and try it out. The paper that describes is is linked below.

Reference:

Pybus M., Dall’Olio G.M., Luisi P., Uzkudun M., Carreno-Torres A., Pavlidis P., Laayouni H., Bertranpetit J. & Engelken J. (2013). 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans, Nucleic Acids Research, 42 (D1) D903-D909. DOI:

Video Tip of the Week: list of genes associated with a disease

I am currently in Puerto Varas, Chile at an EMBO genomics workshop. The workshop is mainly for grad students and the instructors are, for the most part, alumni of the Bork group. I gave a tutorial on genomics databases.

Anyway, the last two days of the workshop is a challenge, in teams of 3-4 advised by an instructor, students are to develop a list of genes associated with epilepsy. Obviously, this could be a trivial task, just go to OMIM or GENECARDS and grab a list. But this challenge requires them to go behind that and use the available data and make predictions. My team attempted, on my suggestion, some brainstorming techniques to ensure a more creative solution than they could come up with individually or just jumping into normal group dynamics. It seemed to work, their solution was quite creative and we will find out today how that worked.

That was my long way of saying, in the process we came across many databases of gene-disease information. above you will find a video of rat gene disease associations from RGD, often used of course to investigate human gene disease associations.

Below you will find a list of some excellent databases and resources to find similar lists:

Gene Association Database  http://geneticassociationdb.nih.gov/

G2D http://g2d2.ogic.ca

OMIM http://www.omim.org

Diseases http://diseases.jensenlab.org/

GeneCards http://genecards.org

DisGeNET http://ibi.imim.es/web/DisGeNET/

Several NCBI resources http://www.ncbi.nlm.nih.gov/guide/howto/find-gen-phen/

UCSC Genome Browser’s tracks for disease and phenotype http://genome.ucsc.edu

There are several others I’m sure, if you have a favorite not on this list, please comment.

Reference for RGD:
Laulederkind S.J.F., Hayman G.T., Wang S.J., Smith J.R., Lowry T.F., Nigam R., Petri V., de Pons J., Dwinell M.R. & Shimoyama M. & (2013). The Rat Genome Database 2013–data, tools and users, Briefings in Bioinformatics, 14 (4) 520-526. DOI:

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Want.

What’s the Answer? (PPI images in compartments)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar 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 BioStar.

This week’s highlighted question is another one of my favorite types–looking for better visualization tools to represent some data features. This time it’s protein-protein interactions (PPI), but organized on the graphical view to show different locations where they are occurring. Maybe it’s nuclear and cytoplasm, maybe it’s Golgi, maybe mitochondria, etc. I’ve seen some graphics like this and I get the utility. And IPA (we assume is the Ingenuity software) can do this it seems–but not everyone will have access to that. An open-source option would be great. But I haven’t tried to make them myself so I was interested to see the suggestions.

Hi,

I am able to create decent PPI network pictures with cytoscape. But I recently noticed that IPA can produce nice visual of networks with membranes, cytoplasm, nucleus i.e. it shows different cellular location of proteins as well as interaction between them. But is there any free software that can produce nice visual of PPI along with such cellular components?

I would also like to know which free software do you use to create stunning visuals of networks.

Any comments will be greatly helpful.

Thanks Diwan

Go have a look at the suggestions. But if you know of some others that would be great too, do share.