Archivo de la etiqueta: UCSC Genome Browser

Newly updated Quick Reference Card

Vídeo Consejo de la semana: UCSC Genome Browser en la nube,,en,GBIC,,yo (GBIC)

Newly updated Quick Reference CardFor all the years we’ve been out doing training on the UCSC Genome Browser tools, we could watch the evolution of the needs of the researchers and the corresponding features of the UCSC Genome Browser site. Al principio, people just needed access to the public data. But then they needed ways to add their own data to the public data context and share the views. UCSC gave us custom tracks, and they gave us browser sessions. Woot!

Cada vez más, the data sets got bigger and more complex and custom tracks couldn’t handle the volume. UCSC delivered track hubs. Woot!

Some people were telling us that they had patient data that they couldn’t load on to the UCSC site because of privacy and legal issues. Then UCSC delivered GBIB–Navegador Genoma in a Box. You could download a local copy of the browser and use your own data behind your firewall.

All of these strategies continue to help users combine their own data with the public data and visualize what they want to show. But there’s also another way now–GBIC, Genome Browser in the Cloud. This week’s tip shows you the video the team created to help people to understand what the GBIC can do. There’s additional information about the features that you can see on their announcement, via the mailing list. But just quickly, here’s the nutgraf:

Hasta ahora, genomics research groups working with sensitive medical data were largely limited to using local Genome Browser installations to maintain confidentiality, complicating data-sharing among collaborators. Hoy, the Genome Browser group of the UC Santa Cruz Genomics Institute announced they have changed that by launching a new product, Genome Browser in the Cloud (GBiC). GBiC introduces new freedom to collaborate by allowing rapid Browser installation, in a UNIX-based cloud or UNIX-virtualized cloud.

And here you can have a look at how it works.

Además, we’ve recently updated our popular Tarjetas de referencia rápida, and we added the note that the GBIC can be used to help people work with their own data. You can download those cards, or get some printed ones, from our website. These cards have had to keep evolving over the years to keep up with all the important features that UCSC adds regularly.

Try out the GBIC with your own data. And they are always looking for feedback on how it suits your needs, or other things you might need. Help them evolve.

Revelación: UCSC Genome Browser tutorials and materials are freely available because UCSC patrocinadores us to do training and outreach on the UCSC Genome Browser.

De referencia:
Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Navarro Gonzalez J, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, and Kent WJ. La UCSC Genome Browser base de datos: 2017 actualización. Nucleic Acids Res. 2016 Noviembre 29;. Palabras: 27899642; PMC: PMC5210591.

Viernes SNPpets

This week we find that all biology is computational biology. And that coding is missing. And I loved the knitted example of chromosomes–knitting is code. También, some new misuse of data, and new appropriate uses. Get a fungus mug. Patients are going to be getting data, but nobody in the public knows about it. Es un secreto.


SNPpets_2Bienvenido a nuestra colección de enlaces Viernes función: SNPpets. Durante la semana nos encontramos con un montón de enlaces y lecturas que nos parecen interesantes, pero no llegar a una entrada de blog. Aquí están para su disfrute…


comprobar que uno de pío incrustado demasiado

Viernes SNPpets

This week I gave a pub talk on the UCSC Genome Browser. It was the first time I’d tried a more general-public version of this. It was huge fun. And it was great timing to have this example of 5000+ samples from autism families to make the case about how hard it is to visualize all this data we are getting. But I also talked about microbes. I even mentioned to goat genome. The benefits and the trip-wires of misuse of personalized data were covered. We touched on restoration of extinct species. So it was a lot like this post, en realidad…. But I didn’t have the threat to GINA until today. Abajo–I would like to have included that. I can’t believe we’re back there.


SNPpets_2Bienvenido a nuestra colección de enlaces Viernes función: SNPpets. Durante la semana nos encontramos con un montón de enlaces y lecturas que nos parecen interesantes, pero no llegar a una entrada de blog. Aquí están para su disfrute…


SNPpets_2

Viernes SNPpets

This week’s SNPpets have a pretty typical list of both new and updated sites and tools. The wheat genome (not gluten-free). A couple of key bits for folks who are scripting calls to NCBI (need to use https soon), or for folks in Asia who could use a UCSC Genome Browser mirror site closer to their location: http://genome-asia.ucsc.edu/. But my favorite thing this week was the best postdoc ad on twitter evah–see the snake one.


SNPpets_2Bienvenido a nuestra colección de enlaces Viernes función: SNPpets. Durante la semana nos encontramos con un montón de enlaces y lecturas que nos parecen interesantes, pero no llegar a una entrada de blog. Aquí están para su disfrute…


https://twitter.com/Sara_and_Snakes/status/742891484064546816

UCSC Genome Bioinformatics

Vídeo Consejo de la semana: UCSC Genome Browser Exon modo de sólo,en

El equipo de UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “multi-region” option. When it was first launched, I did a tip on how to use that, with some of the things that I noticed while I was testing it pre-launch. But now the folks at UCSC have their own video on the exon-only display that you might also find useful.

One of the things that is illustrated here is how the exon-only mode is handy to enhance your exploration of RNA-Seq data. It also uses a great CODIFICAR data set as an example, and if you haven’t been using that collection it’s a good reminder of the kinds of things you can find in that resource still. And this extensive data set shows how much easier it is to look at different isoforms in the data in this new exon-only mode.

So have a look at this display option if you haven’t before, especially how it can help you to see transcript differences. Si usted no está familiarizado con el Codifica los datos that’s being used, you can also see our training on that which will help you to understand how to use that data and the filtering features that are also used in this video.

Nota especial: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look.

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Revelación: UCSC Genome Browser tutorials are freely available because UCSC patrocinadores us to do training and outreach on the UCSC Genome Browser.

Enlaces rápidos:

UCSC Genome Browser: http://genome.ucsc.edu

UCSC Genome Browser training materials: http://openhelix.com/ucsc

CODIFICAR: http://www.openhelix.com/ENCODE2

Referencias:

Espolón, M., Rama, A., Rosenbloom, K., Raney, B., Patrocinadores, B., Nejad, P., Sotavento, B., Aprendido, K., Karolchik, D., Hinrichs, A., Heitner, S., Duro, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Peluquero, G., Haussler, D., Kuhn, R., & Kent, En. (2016). La UCSC Genome Browser base de datos: 2016 actualización Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

El proyecto ENCODE Consorcio (2012). Una enciclopedia de elementos de ADN integrado en el genoma humano Naturaleza, 489 (7414), 57-74 DOI: 10.1038/nature11247

sneakPeekGateway

Vídeo Consejo de la semana: New UCSC Genome Browser Gateway look

sneakPeekGateway

For years now we’ve been doing training and outreach on the UCSC Genome Browser. And there’s been a lot of change over the years–so much more data, so many new tools, nuevas especies. All that ENCODE information and a portal para que. But the look of the main site was largely the same. Here’s a post we did that included the UCSC site traffic in 2000, and another time we took a look at the old style interface ~2004. And there was the switch to the new blue look in 2012.

Sin embargo, the main gateway page was largely the familiar look. The gateway–where you begin to do most text-based or region-based queries for a species–was mostly altered only with some additional buttons and options. And an increasingly long list of species to choose from. Pero ahora–it’s time to look again. The gateway is very different today. You’ll have faster and easier access to get started when you go to the site, and new ways to engage with the data that you want to begin to access.

There are additional details on the UCSC landing page in the News area, including credits to the development team involved. The other key pieces include some relocations of the previous button options:

Note that a few browser utilities that were previously accessed through links and buttons on the Gateway page have been moved to the top menu bar:

*Browser reset: Genome Browser > Reset All User Settings
*Track search: Genome Browser > Track Search
*Add custom tracks: My Data > Temas personalizados
*Track hubs: My Data > Hubs pista
*Configure las pistas y la pantalla: Genome Browser > Configure

The UCSC team has created a short intro video to the new look. That is our Video Tip of the Week:

Por supuesto, this means we’ll need to update our slides and exercises. We like things to stabilize a bit after a rollout to be sure things are solid. But soon we’ll include the new navigation in our materials.

The underlying ways to access the particular assembly features you need for a given genome, and the data for your tracks of interest, is unchanged. So those parts of our training materials will still help you to get the most out of your searches. We’ll let you know when we’ve made the changes to the materials as well.

 

Enlaces rápidos:

UCSC Genome Browser main landing page: http://genome.ucsc.edu

Training materials:

Intro: http://openhelix.com/ucsc

Avanzada: http://openhelix.com/ucscadv

De referencia:

Espolón, M., Rama, A., Rosenbloom, K., Raney, B., Patrocinadores, B., Nejad, P., Sotavento, B., Aprendido, K., Karolchik, D., Hinrichs, A., Heitner, S., Duro, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Peluquero, G., Haussler, D., Kuhn, R., & Kent, En. (2015). La UCSC Genome Browser base de datos: 2016 actualización Nucleic Acids Research DOI: 10.1093/nar/gkv1275

Revelación: UCSC Genome Browser tutorials are freely available because UCSC patrocinadores us to do training and outreach on the UCSC Genome Browser.

SNPpets_2

Viernes SNPpets

This week’s SNPpets include something unusual: bioinformatics software becoming a mainstream discussion. A recent NYT piece about Zika genomics included a Bandage software-based illustrations, and a subsequent explainer piece in SciAm covered it. Zika was big this week. Por supuesto, we covered Bandage months ago…. A reprise and riff of Tardigate was good reading. Also this week: GBrowse for peanut, FireBrowse for the Broad, updates to manía generada, Galaxia record hit, and the opposite of update: UCSC Genome Browser in ASCII. Impersonal genomics made me laugh.


SNPpets_2Bienvenido a nuestra colección de enlaces Viernes función: SNPpets. Durante la semana nos encontramos con un montón de enlaces y lecturas que nos parecen interesantes, pero no llegar a una entrada de blog. Aquí están para su disfrute…


UCSC Genome Browser new feature

Vídeo Consejo de la semana: Multi-region visualization in the UCSC Genome Browser

This week’s video tip demonstrates a new feature at the UCSC Genome Browser. I think it’s kind of unusual, and conceptually took me a little while to get used to when I started testing it. So I wanted to go over the basics for you, and give you a couple of tips on things that I had to grok as I got used to this new visualization option.

La headline for the news item describes it as: “Combine Multiple Regions of the Genome Browser into a Single Visualization!” y

Have you ever wished you could remove all of the intronic or intergenic regions from the Genome Browser display? Have you ever dreamed of being able to visualize multiple far-flung regions of a genome? Bueno, now you can with the new “multi-region” option in the Genome Browser!

I should probably start with the first thing that confused me–the name “multi-region”. I thought that I was going to be able to see maybe part of a region on chromosome 1, and something on chromosome 8, maybe at the same time. But that’s not how this works. En este caso, you look at multiple regions along the same chromosome, with some of the intervening sequences snipped out. This creates a sort of “virtual chromosome” for you to interact with.

En el video de esta semana, I’ll show you how that looks using the BRCA1 gene. First I show how you can look at all the exons together–with introns clipped out. And then I show how you can see the genes in the neighborhood displayed together, with the non-coding regions clipped out. These are 2 of the separate options for viewing.

Yo uso el “Ver” menu option to illustrate this feature. But there is another way to access it–you can use the “multi-region” button in the browser buttons area.

multiregion_button

To keep the video short, I didn’t go into every detail on this tool. Usted debe revisar la news announcement for it, and the link to the additional details in the User Guide documentation para más. The new feature is also mentioned briefly in the lastest NAR paper on the UCSC Genome Browser (relacionados a continuación). And you should try it out, por supuesto! That’s the best way to really understand how it might help you to visualize regions of the genome that you might be interested in.

Also as in the news, thanks to the development team. I am always looking for new visualizations, and this fun to test!

Thank you to Galt Barber, Mateo Speir, and the entire UCSC Genome Browser quality assurance team for all of their efforts in creating these exciting new display modes.

Follow UCSC on Twitter:

Enlaces rápidos:

UCSC Genome Browser: genome.ucsc.edu

News item on multi-region: http://genome.ucsc.edu/goldenPath/newsarch.html#030816

Training materials on the UCSC Genome Browser: http://openhelix.com/ucsc

De referencia:

Espolón, M., Rama, A., Rosenbloom, K., Raney, B., Patrocinadores, B., Nejad, P., Sotavento, B., Aprendido, K., Karolchik, D., Hinrichs, A., Heitner, S., Duro, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Peluquero, G., Haussler, D., Kuhn, R., & Kent, En. (2016). La UCSC Genome Browser base de datos: 2016 actualización Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

Revelación: UCSC Genome Browser tutorials are freely available because UCSC patrocinadores us to do training and outreach on the UCSC Genome Browser.

one query type from: genomeportal.stanford.edu/pan-tcga/

Consejo del la Semana: El Explorador de Clínica del Genoma del Cáncer Atlas

Acceso a TCGA cancer data has been approached in a variety of ways. This week’s tip of the week highlights a web-based portal for improved access to the data in different ways. The Stanford Cancer Genome Atlas Clinical Explorer is aimed at helping identify clinically relevant genes in the cancer data sets.

They note that the data is available in other places and tools, from tools we’ve talked about before such as cBioPortal, UCSC Browser Genómica del Cáncer, and interacting with the StratomeX características. But this portal helps peoplt to quickly focus on clinical parameters in ways that aren’t as straightforward in the other tools.

You can learn more about the project on their site from their Overview en el sitio, and you can see their publication about it (a continuación). The paper also covers some issues they had with the downloaded data that might be worth noting. And they also supplemented their analysis and information with COSMIC y OBJETIVO (tumor unalterations relevant for genomics-driven therapy) datos, así.

one query type from: genomeportal.stanford.edu/pan-tcga/

One query type from: genomeportal.stanford.edu/pan-tcga/

The interface offers several quick ways to dive into the data.

Hay 3 main query types: genes associated with certain clinical parameters; query directly by gene/protein/miR; and a two-hit hypothesis test. The first query is the image I’ve shown here. When you get to the the results, you can explore them in more detail with sortable tabular outputs, and on gene pages tabs for copy number changes, mutaciones, and RNA-seq values.

They give you some “example queries” that you can use as a way to get started and see what’s available underneath. And although we usually like to highlight a video, the tutorial that they provide is a slide embed.

So have a look at this interface if you’d like to explore TCGA data with a handy and quick query strategy. It might offer some hunting license on genes you are interested in, or some ideas for other investigations in tumor types you study.

 

Enlace rápido:

Stanford-TCGA-CE: http://genomeportal.stanford.edu/pan-tcga

De referencia:
Sotavento, H., Palm, J., Grimes, S., & Su, H. (2015). El Explorador de Clínica del Genoma del Cáncer Atlas: a web and mobile interface for identifying clinical–genomic driver associations Genoma Medicina, 7 (1) DOI: 10.1186/s13073-015-0226-3

SNPpets_2

Viernes SNPpets

This week’s SNPpets cover a range of issues. Attempting to community-curate bioinformatics tools, a new paper on UCSC Genome Browser‘s features, iplant now reborn as CyVerse, errors in databases, personalized diagnosis from the UK 100000 Genomas del proyecto and the re-launch of their PanelApp, and some new plant tools: AgroPortal y 30 plants going into OrothoDB. También, read those thesis submissions carefully. There may be an easter egg.


SNPpets_2Bienvenido a nuestra colección de enlaces Viernes función: SNPpets. Durante la semana nos encontramos con un montón de enlaces y lecturas que nos parecen interesantes, pero no llegar a una entrada de blog. Aquí están para su disfrute…