标记档案: UCSC基因组浏览器

Newly updated Quick Reference Card

一周的视频提示: UCSC基因组浏览器的云,,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. 起初, 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给了我们自定义的轨道,,en,他们给了我们,,en,浏览器会话,,en,该数据集变得更大,更复杂和定制的曲目无法处理量,,en,UCSC交付,,en,轨道枢纽,,en,一些人告诉我们,他们有患者数据,他们不能在负载由于隐私问题和法律问题的UCSC网站,,en,然后UCSC交付GBIB,,en,你可以下载浏览器的本地副本,并使用自己的数据在防火墙后面,,en,所有这些策略都将继续帮助用户与公共数据结合自己的数据和可视化,他们想显示什么,,en,但也有另一种现在路,,en,云中的基因组浏览器,,en,本周将向您展示视频创建的团队来帮助人们了解什么GBIC可以做,,en, and they gave us browser sessions. 活泉!

越来越多, the data sets got bigger and more complex and custom tracks couldn’t handle the volume. UCSC delivered track hubs. 活泉!

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–在一箱基因组浏览器. 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. 有一个关于该功能的其他信息,,en,你可以在自己的公告看,,en,通过邮件列表,,en,但就迅速,,en,这里的nutgraf,,en,基因组学研究组与敏感的医疗数据的工作大多只能使用当地的基因组浏览器的安装维护保密,,en,复杂的数据共享协作者之间,,en,在加州大学圣克鲁斯分校基因组研究所的基因组浏览器小组宣布,他们已经改变了,通过推出新产品,,en,GBIC,,yo,GBIC引入了新的自由度,允许快速的浏览器安装合作,,en,在基于UNIX的云或UNIX的虚拟化云,,en,在这里,你可以看看它是如何工作,,en,我们最近更新了流行,,en,我们补充说,GBIC可以用来帮助人们与他们自己的数据的工作笔记,,en you can see on their announcement, via the mailing list. But just quickly, here’s the nutgraf:

到目前为止, 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. 今天, 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.

此外, we’ve recently updated our popular 快速参考卡, and we added the note that the GBIC can be used to help people work with their own data. 您可以下载这些卡,,en,或得到一些印刷者,,en,从我们的网站,,en,这些卡都必须保持不断发展,多年来跟上所有重要功能,UCSC会定期增加,,en,尝试一下GBIC与自己的数据,,en,他们一直在寻找反馈,它是如何满足您的需求,,en,或者其他的东西,你可能需要,,en,帮助他们发展,,en,UCSC基因组浏览器教程和材料都是免费的,因为UCSC,,en,泰纳ç,,en,理发GP,,en,卡斯帕Ĵ,,en,Diekhans中号,,en,菲舍尔CM,,de,ð吉布森,,fr,纳瓦罗·冈萨雷斯Ĵ,,es,Heitner小号,,en,李BT,,en,李CM,,en,内贾德P,,en,比利亚雷亚尔ç,,es,维维安Ĵ,,es,和肯特WJ,,en,PMC,,en,PMC5210591,,zh-CN, 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.

披露: UCSC Genome Browser tutorials and materials are freely available because UCSC 赞助商 us to do training and outreach on the UCSC Genome Browser.

参考:
Tyner C, Barber GP, Casper J, 克劳森ħ, Diekhans M, 艾森哈特Ç, Fischer CM, Gibson D, Navarro Gonzalez J, Guruvadoo L, Haeussler M, Heitner S, Hinrichs先生作为, Karolchik Ð, Lee BT, Lee CM, Nejad P, 雷尼BJ, 罗森布鲁姆KR, Speir ML, Villarreal C, Vivian J, 茨威格的AS, 豪斯勒ď的, 库恩室, and Kent WJ. UCSC基因组浏览器数据库: 2017 更新. 核酸水库. 2016 十一月 29;. PMID: 27899642; PMC: PMC5210591.

星期五SNPpets

本周,我们发现,所有的生物是计算生物学. 和编码缺失. 我爱染色体的针织例子–针织是代码. 还, 数据的一些新的滥用, 和新的正确用法. 获取木耳杯. 患者将要获取数据, 但没有人在公众知道它. 这是个秘密.


SNPpets_2欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…


检查一个嵌入式鸣叫太

星期五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, 其实…. But I didn’t have the threat to GINA until today. 向下–I would like to have included that. I can’t believe we’re back there.


SNPpets_2欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…


SNPpets_2

星期五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基因组浏览器 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_2欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…


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

UCSC Genome Bioinformatics

一周的视频提示: UCSC基因组外显子的浏览器仅模式,en

球队在 UCSC基因组浏览器 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 “多区域” 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 进行编码 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. 如果你不熟悉的 编码资料 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.

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

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

披露: UCSC Genome Browser tutorials are freely available because UCSC 赞助商 us to do training and outreach on the UCSC Genome Browser.

快速链接:

UCSC基因组浏览器: http://genome.ucsc.edu

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

进行编码: 銈://www.openhelix.com/ENCODE2

参考文献:

带动, 米, 科, 答:, 罗森布鲁姆, 光, 雷尼, 二, 赞助商, 二, Nejad, 体育, 李, 二, 学习, 光, Karolchik, 四, Hinrichs先生, 答:, 海特纳, 学, 硬, 河, Haeussler, 米, Guruvadoo, 属, 藤田, 体育, Eisenhart, 三, Diekhans, 米, 克劳森, 阁下, 卡斯帕, j的, 理发, 克, 豪斯勒速度, 四, 库恩, 河, & 肯特, 在. (2016). UCSC基因组浏览器数据库: 2016 更新 核酸研究, 44 (D1) 分类号: 10.1093/nar/gkv1275

ENCODE项目联盟 (2012). 一个集成的人类基因组中的DNA元件的百科全书 自然, 489 (7414), 57-74 分类号: 10.1038/nature11247

sneakPeekGateway

一周的视频提示: New UCSC Genome Browser Gateway look

sneakPeekGateway

For years now we’ve been doing training and outreach on the UCSC基因组浏览器. And there’s been a lot of change over the years–so much more data, so many new tools, 新种. All that ENCODE information and a portal 该. 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.

不过, 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. 但现在–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.

有在新闻领域的UCSC登陆页面上的其他详细信息, 包括信贷所涉及的开发团队. 另一个关键部分包括以前的按钮选择一些重定位:

需要注意的是,以前通过网关页面上的链接和按钮访问的几个浏览器工具被移到了顶部的菜单栏:

*浏览器复位: 基因组浏览器 > 重置所有用户设置
*曲目搜索: 基因组浏览器 > 音轨搜索
*添加自定义轨道: 我的数据 > 自定义跟踪
*Track hubs: 我的数据 > 轨道枢纽
*配置跟踪和显示: 基因组浏览器 > 配置

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

当然, 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.

 

快速链接:

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

Training materials:

简介: http://openhelix.com/ucsc

进阶: http://openhelix.com/ucscadv

参考:

带动, 米, 科, 答:, 罗森布鲁姆, 光, 雷尼, 二, 赞助商, 二, Nejad, 体育, 李, 二, 学习, 光, Karolchik, 四, Hinrichs先生, 答:, 海特纳, 学, 硬, 河, Haeussler, 米, Guruvadoo, 属, 藤田, 体育, Eisenhart, 三, Diekhans, 米, 克劳森, 阁下, 卡斯帕, j的, 理发, 克, 豪斯勒速度, 四, 库恩, 河, & 肯特, 在. (2015). UCSC基因组浏览器数据库: 2016 更新 核酸研究 分类号: 10.1093/nar/gkv1275

披露: UCSC Genome Browser tutorials are freely available because UCSC 赞助商 us to do training and outreach on the UCSC Genome Browser.

SNPpets_2

星期五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. 当然, 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, 星系 record hit, and the opposite of update: UCSC基因组浏览器 in ASCII. Impersonal genomics made me laugh.


SNPpets_2欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…


UCSC Genome Browser new feature

一周的视频提示: Multi-region visualization in the UCSC Genome Browser

本周的视频尖在演示了一个新功能 UCSC基因组浏览器. I think it’s kind of unusual, 和概念上我花了一些时间来习惯,当我开始测试它. 所以,我想去过的基础知识为你, 给你一对夫妇的事情的提示,我不得不为神交我习惯了这种新的可视化选项.

标题的新闻项目 将其描述为: “结合基因组浏览器的多个区域为单幅可视化!” 和

你是否曾经希望能够从基因组浏览器显示删除所有内含子或间隔区的? 你是否曾经梦想能够可视化基因组的多遥远的地区? 嗯, 现在你可以用新 “多区域” 在基因组浏览器选项!

我也许应该开始与困惑我的第一件事情–名字 “多区域”. 我以为我将能够看到一个地区的染色体上的部分可能 1, 和一些染色体 8, 也许在同一时间. 但是,这不是如何运作. 在这种情况下, 你看多个区域沿同一染色体, 与某些间插序列的剪断出. 这将创建一个排序 “虚拟染色体” 为你互动.

在本周的视频, 我会告诉你如何看起来使用的BRCA1基因. 首先,我告诉你如何可以在所有外显子一起看–与内含子剪辑了. 然后,我告诉你如何看基因一起显示附近, 与非编码区裁剪出. 这些都是 2 用于查看单独的选项.

我用的是 “查看” 菜单选项来说明这个功能. 但还有另一种方式来访问它–您可以使用 “多区域” 按钮,在浏览器按钮区域.

multiregion_button

为了保持视频短片, 我没去到每一个细节上这个工​​具. 你应该检查出 消息公布吧, 并链接到的其他详细信息 用户指南文档 更多. 新的功能也在介绍最新NAR简要提到在UCSC基因组浏览器 (下面链接). 你应该尝试一下, 当然! 这是真正了解它如何帮助你想象,你可能会感兴趣的基因组区域的最佳方式.

也如在新闻, 由于开发团队. 我一直在寻找新的可视化, 而这个有趣的测试!

谢谢高尔特理发, 马修·斯皮尔, 而整个UCSC基因组浏览器的质量保证团队,为所有的努力在创造这些激动人心的新的显示模式.

按照加州大学圣克鲁兹分校的Twitter:

快速链接:

UCSC基因组浏览器: genome.ucsc.edu

多区域新闻项目: http://genome.ucsc.edu/goldenPath/newsarch.html#030816

在UCSC基因组浏览器培训教材: http://openhelix.com/ucsc

参考:

带动, 米, 科, 答:, 罗森布鲁姆, 光, 雷尼, 二, 赞助商, 二, Nejad, 体育, 李, 二, 学习, 光, Karolchik, 四, Hinrichs先生, 答:, 海特纳, 学, 硬, 河, Haeussler, 米, Guruvadoo, 属, 藤田, 体育, Eisenhart, 三, Diekhans, 米, 克劳森, 阁下, 卡斯帕, j的, 理发, 克, 豪斯勒速度, 四, 库恩, 河, & 肯特, 在. (2016). UCSC基因组浏览器数据库: 2016 更新 核酸研究, 44 (D1) 分类号: 10.1093/nar/gkv1275

披露: UCSC Genome Browser tutorials are freely available because UCSC 赞助商 us to do training and outreach on the UCSC Genome Browser.

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

提示的周: 癌症基因组图谱的临床资源管理器

访问 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, 肿瘤基因组学UCSC的浏览器, and interacting with the StratomeX 功能. 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 在现场, and you can see their publication about it (下面). 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 宇宙目标 (umor lterations relevant for GEnomics-driven herapy) 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.

有 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, 突变, 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.

 

快速链接:

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

参考:
李, 阁下, Palm, j的, Grimes, 学, & 这, ħ. (2015). 癌症基因组图谱的临床资源管理器: a web and mobile interface for identifying clinical–genomic driver associations 基因组医学, 7 (1) 分类号: 10.1186/s13073-015-0226-3

SNPpets_2

星期五SNPpets

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


SNPpets_2欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…