الوسم المحفوظات: UCSC متصفح الجينوم

Newly updated Quick Reference Card

تلميح فيديو للأسبوع: متصفح UCSC الجينوم في الغيمة,,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. في البداية, 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!

على نحو متزايد, 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–متصفح الجينوم في صندوق. 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:

حتى الآن, 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. اليوم, 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.

وبالإضافة إلى ذلك, we’ve recently updated our popular بطاقات مرجع سريع, 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.

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

مرجع:
Tyner C, Barber GP, Casper J, كلوسون 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, راني BJ, روسنبلووم KR, Speir ML, Villarreal C, Vivian J, تسفايغ AS, هاوسلر D, كن RM, and Kent WJ. مستعرض قاعدة بيانات الجينوم UCSC: 2017 التحديث. الأحماض النووية بحوث. 2016 نوفمبر 29;. PMID: 27899642; PMC: PMC5210591.

الجمعة SNPpets

هذا الأسبوع نجد أن كل علم الأحياء هو علم الأحياء الحسابي. وأن الترميز في عداد المفقودين. وأنا أحب المثال محبوك من الكروموسومات–الحياكة هي متاحة. أيضا, بعض سوء استخدام جديد لبيانات, والاستخدامات المناسبة جديدة. الحصول على القدح الفطر. المرضى سوف يكون الحصول على البيانات, ولكن لا أحد في الجمهور يعرف عنه. إنه سر.


SNPpets_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…


تأكد من أن واحد لسقسقة جزءا لا يتجزأ من

الجمعة 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, في الواقع…. But I didn’t have the threat to GINA until today. للأسف–I would like to have included that. I can’t believe we’re back there.


SNPpets_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…


SNPpets_2

الجمعة 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 متصفح الجينوم 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_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…


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

UCSC Genome Bioinformatics

تلميح فيديو للأسبوع: الوضع UCSC الجينوم متصفح اكسون فقط,en

الفريق في UCSC متصفح الجينوم 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 ترميز 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. إذا كنت لم تكن مألوفة مع ترميز البيانات 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.

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

+++++++++++++

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

وصلات سريعة:

UCSC متصفح الجينوم: http://genome.ucsc.edu

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

ترميز: المتشعب://www.openhelix.com/ENCODE2

المراجع:

مهماز, م., فرع, أ., Rosenbloom, ك., راني, ب., مقدمي, ب., Nejad, P., لي, ب., المستفادة, ك., Karolchik, د., Hinrichs, أ., Heitner, س., الثابت, ر., Haeussler, م., Guruvadoo, L., فوجيتا, P., Eisenhart, C., Diekhans, م., كلوسون, ه., كاسبر, ج., حلاق, غ., هاوسلر, د., كوهن, ر., & كينت, في. (2016). مستعرض قاعدة بيانات الجينوم UCSC: 2016 التحديث أبحاث الأحماض النووية, 44 (D1) دوى: 10.1093/nar/gkv1275

الكونسورتيوم مشروع ترميز (2012). موسوعة متكاملة من عناصر DNA في الجينوم البشري طبيعة, 489 (7414), 57-74 دوى: 10.1038/nature11247

sneakPeekGateway

تلميح فيديو للأسبوع: New UCSC Genome Browser Gateway look

sneakPeekGateway

For years now we’ve been doing training and outreach on the UCSC متصفح الجينوم. And there’s been a lot of change over the years–so much more data, so many new tools, الأنواع الجديدة. All that ENCODE information and a portal لذلك. 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.

ومع ذلك, 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. ولكن الآن–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: الجينوم المستعرض > Reset All User Settings
*Track search: الجينوم المستعرض > Track Search
*Add custom tracks: My Data > عرف المسارات
*Track hubs: My Data > المسار موزع
*تكوين وعرض المسارات: الجينوم المستعرض > Configure

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

بالطبع, 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.

 

وصلات سريعة:

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

Training materials:

مقدمة: http://openhelix.com/ucsc

متقدم: http://openhelix.com/ucscadv

مرجع:

مهماز, م., فرع, أ., Rosenbloom, ك., راني, ب., مقدمي, ب., Nejad, P., لي, ب., المستفادة, ك., Karolchik, د., Hinrichs, أ., Heitner, س., الثابت, ر., Haeussler, م., Guruvadoo, L., فوجيتا, P., Eisenhart, C., Diekhans, م., كلوسون, ه., كاسبر, ج., حلاق, غ., هاوسلر, د., كوهن, ر., & كينت, في. (2015). مستعرض قاعدة بيانات الجينوم UCSC: 2016 التحديث أبحاث الأحماض النووية دوى: 10.1093/nar/gkv1275

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

SNPpets_2

الجمعة 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. بالطبع, 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 GeneMania, المجرة record hit, and the opposite of update: UCSC متصفح الجينوم in ASCII. Impersonal genomics made me laugh.


SNPpets_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…


UCSC Genome Browser new feature

تلميح فيديو للأسبوع: Multi-region visualization in the UCSC Genome Browser

This week’s video tip demonstrates a new feature at the UCSC متصفح الجينوم. 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.

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

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? جيد, 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. في هذه الحالة, 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.

في الفيديو هذا الأسبوع, 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. وهذه هي 2 of the separate options for viewing.

يمكنني استخدام “رأي” 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. You should check out the news announcement for it, and the link to the additional details in the User Guide documentation لمزيد من. The new feature is also mentioned briefly in the lastest NAR paper on the UCSC Genome Browser (ترتبط أدناه). And you should try it out, بالطبع! 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, ماثيو 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:

وصلات سريعة:

UCSC متصفح الجينوم: 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

مرجع:

مهماز, م., فرع, أ., Rosenbloom, ك., راني, ب., مقدمي, ب., Nejad, P., لي, ب., المستفادة, ك., Karolchik, د., Hinrichs, أ., Heitner, س., الثابت, ر., Haeussler, م., Guruvadoo, L., فوجيتا, P., Eisenhart, C., Diekhans, م., كلوسون, ه., كاسبر, ج., حلاق, غ., هاوسلر, د., كوهن, ر., & كينت, في. (2016). مستعرض قاعدة بيانات الجينوم UCSC: 2016 التحديث أبحاث الأحماض النووية, 44 (D1) دوى: 10.1093/nar/gkv1275

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

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

نصيحة الأسبوع: The Cancer Genome Atlas Clinical Explorer

الوصول 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 مستعرض جينوم السرطان, and interacting with the StratomeX ملامح. 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 في الموقع, and you can see their publication about it (أقل من). 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 و TARGET (رumor alterations relevant for شركة جنرال الكتريكnomics-driven رherapy) data as well.

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.

يوجد 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, الطفرات, 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.

 

ربط سريع:

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

مرجع:
لي, ه., Palm, ج., Grimes, س., & لها, H. (2015). The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical–genomic driver associations الجينوم الطب, 7 (1) دوى: 10.1186/s13073-015-0226-3

SNPpets_2

الجمعة SNPpets

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


SNPpets_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…