分类存档: 提示的周


一周的视频提示: Direct to Consumer Genetic Testing and Genetic Counselling

在OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, 我知道, it still varies). But outreach really is getting better. There are journals now that are also enforcing more reader-friendly ways to describe the research, with non-jargon summaries and some terrific visual aids.

越来越多, there are also videos associated with papers. I just came across this one, and thought it was a nice example of an important issue for non-scientists to access.

So this looks at direct-to-consumer (DTC) services available in Europe, but some of the same ones are available in the US. 当然, 在美国, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. 叹息.



Middleton, 答:, 门德斯, Á., 本杰明, ç. 米, & Howard, ħ. ç. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. 个性化医疗, (14:3) , 页 249-257 , 分类号 10.2217/pme-2017-0001.


一周的视频提示: Neandertal Inheritance and Consequences

确定, it’s been a while since this was a regular feature. But I am still finding that I want to show some videos of science topics and software tools sometimes. So it may not be a regular feature, but I will be highlighting some videos that seem interesting to me for various reasons.

This video struck me because I recently gave a talk about the information from ancestral genomes and the influence of the DNA on us today (as well as how we visualize that). They use software that we’ve talked about before, PolyPhen上海对外贸易学院, in this analysis. And it would have been handy to have this as a resources to give out to the audience members, who were general public folks in a pub. I am impressed that a research team did this additional step of explaining their research in this way.


Dannemann, 米, Prüfer, 光, 瓦格纳, 答:, & 凯尔索, Ĵ. (2017). Functional implications of Neandertal introgression in modern humans 基因组生物学 18:61. 分类号: 10.1186/s13059-017-1181-7


一周的视频提示: 电视空军基地, 并支持模式生物群落的一封信

本周的视频技巧是两件事情提示. 第一, it was a tweet from FlyBase, 他们的视频频道. It’s been a while since we’d done a FlyBase Tip of the Week, so that was enough of a reason.

But it also came just after I was thinking about the importance of the model organisms, based on the campaign by the model organism databases to save their funding. Here’s a tweet from the yeast genome database (新元) with a plea:

But this letter cites yeast, 苍蝇, WormBase, 舞蹈, 麦肯锡, 含RGD基因本体论 以及.

mergeI have a soft spot for model organisms, not only because of the tremendous amount of great biology they’ve provided. I was a postdoc at The Jackson Lab, and I am acutely aware of how crucial it is to have the depth of the species specialists involved in creating and maintaining the resources that are appropriate for their organism. But it’s more than just institutional knowledge and data, 当然. It’s also the importance of the community of researchers working on that organism, supporting them and having their needs met in many ways with species-specific resources.

So this week’s tip highlights some features of the FlyBase tools, as a way to remind folks of the great work that’s going on at model organism databases (MODs).

现在, if you haven’t already done so, please consider signing on to the letter of support for these databases. You can read more about the issue over at the site, but briefly:

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these 自然科学 news stories). While increased integration will present many advantages, the plan will result in a loss of critical organism-specific datasets. The funding cut will also cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs. Given the large number of scientists that this policy change would affect and the importance of their work, this is a matter of extreme concern.

I have always shouted about the importance of high-quality curation. It’s so undervalued, but it’s only more and more crucial now that we are getting so much sequence data and we need the best existing knowledge to help guide us through it. Now is not the time to cut back on curation.

So if you have valued MOD data and community sites, please consider signing on to the letter of support.


FlyBase: http://flybase.org/

Support Model Organism Databases 信: http://www.genetics-gsa.org/MODSupport/


海登, Erica Check. “Funding for model-organism databases in trouble.” 自然新闻. () 分类号: 10.1038/nature.2016.20134

凯撒, Jocelyn. “Funding for key data resources in jeopardy.” 科学 351.6268 (2016): 14-14. 分类号: 10.1126/science.351.6268.14

Attrill, Helen, 等. “FlyBase: establishing a Gene Group resource for Drosophila melanogaster.” 核酸研究 (2015): gkv1046. 分类号: 10.1093/nar/gkv1046


一周的视频提示: Genonets, exploring genotype-phenotype relationships

Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, 表型, and researchers/physicians who may either study or treat the associated medical issues (见 MyGene2 most recently) . But there’s a lot of room upstream of these kinds of patient outcomes to explore genotypes and phenotypes. This week’s Video Tip of the Week is for Genonets, offering “Analysis and Visualization of Genotype Networks”, a tool that can help to explore these relationships for pre-clinical/research scenarios as well.

A recent paper explains the goals behind their tools, and they also have a series of videos on their web site to help you get going with Genonets. I’ll put the intro video here, but be sure to click over to their “Learn Genonets” page for a lot more. There’s also a text-based tutorial you can work through which is helpful.

You can also kick the tires a bit with a sample file that’s available from their search page. Just click the checkbox to load it up and try it out. And then be sure to explore those “deep dives” videos to go further.



Genonets: http://ieu-genonets.uzh.ch


Khalid, 楼, Aguilar-Rodríguez, j的, 瓦格纳, 答:, & 佩恩, Ĵ. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks 核酸研究 分类号: 10.1093/nar/gkw313

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.


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


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


一周的视频提示: MyGene2, 与对方罕见的情况下连接家庭

Last week’s tip encouraged people to think about how their DNA may be used by various stakeholders. This could be researchers, physicians, pharmaceutical companies, 等. But one thing it didn’t really cover–now that I think of it–was connecting with other families who may share variations that impact the health of someone in their household. If there isn’t research, or treatment, this connection alone might be worth it for some families.

So when NPR recently had a story on a database for families with rare genetic conditions, 我去看看: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

该网站是 MyGene2, and it can help unrelated folks who have the same genome challenges connect with each other. It also can connect folks to researchers interested in the topic. But it does seem to be aimed more specifically at families seeking each other. It was recently awarded a chance to compete for the final prize in the Open Science Prize effort, and they got a funding boost to keep going.

有一 “欢迎” video that they’ve made, but it’s light on the software details. 仍, 虽然, I wanted to share the information so families may find it, and researchers may want to know about this resources as well. The video isn’t embeddable, 虽然, so you’ll have to click to view it:


You can learn more about the resources from their FAQ collection. I’ve found a couple of references (下面) that provide some further information about the project [注意:: 的 医学遗传学 one goes to a paywalled, 片–but you can access the pre-print version PDF at bioRxiv]. As more and more families who are seeking answers will have sequencing information available, they’ll need a place to go with that. I hope they find each other, and find answers.


MyGene2: http://www.mygene2.org

按照他们的Twitter: https://twitter.com/MyGene2

Find them on Facebook: https://www.facebook.com/MyGene2/

(该 医学遗传学 piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)


Panko, 乙. (2016). Six finalists to compete for Open Science Prize 科学 分类号: 10.1126/science.aaf9980

Chong, j的, 于, j的, Lorentzen, 体育, 公园, 光, Jamal, 学, Tabor, 阁下, Rauch, 答:, Saenz, 米, Boltshauser, 大肠杆菌, Patterson, 光, 尼克森, 四, & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features 医学遗传学 分类号: 10.1038/gim.2015.161


一周的视频提示: Your DNA, Your Say. GA4GH wants to hear from you. 和你.

基因组学与健康全球联盟 (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the entire sequence information of a patient. It would ask a simple yes/no question about a given sequence variant–and if a “是的” came back, then a researcher could go through the process of getting proper access to protected patient data.

So it was a way to keep people from pawing through data that they don’t need. And yet it could still connect people who might benefit from research, with researchers who need information.

But certainly issues of patient or donor privacy are hot topics. More and more data will come in from large projects, or from diagnostic samples, and cancer vs normal tissue comparisons, and we are going to struggle with the access vs. privacy matters for a while. The general public is only now becoming aware of the impacts. But we certainly need people to understand and we’ll want them to contribute to expanding our knowledge about health and disease.

That’s why the folks associated with GA4GH, the Wellcome Trust, and the Wellcome Genome Campus are eager to engage the public on their feelings on use of genomic sequence data. 他们有 launched a project called “Your DNA Your Say”[PDF格式], in the form of a survey with videos to help understand where people are on this issue. Here’s the intro video to entice you to answer the survey:

I answered the survey because I do have concerns about access to information that will help us drive the science forward, as well as about the potential for misuse of the information. But I would like them to hear from as many people as possible, so that we can understand the barriers to research and donation that are looming. Have your say. 传播消息.

You can learn more about their ideas in a variety of publications–I’ll link to one below, but there are other publications and more details about the overall projects and individual tools at the GA4GH web site.


Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/


Lawler, 米, Siu, 属, 雷姆, 阁下, Chanock, 学, Alterovitz, 克, Burn, j的, 卡尔沃, 楼, Lacombe, 四, 这些, 二, 北, 光, Sawyers, 三, & , . (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health Cancer Discovery, 5 (11), 1133-1136 分类号: 10.1158/2159-8290.CD-15-0821


一周的视频提示: ProSplign在NCBI的基因组工作台,en


There are many tools at NCBI的, with a huge range of functions. 文学, 序列数据, 变化, 蛋白质结构, chemicals and bioassays, 多. It’s hard to keep track of what’s available. Their video tutorials are helping me to be aware of new tools, and new features within existing tools. 本周的周提示, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.

虽然 基因组工作台 itself has been around for a while (we featured it as a tip it first in 2013), it is constantly underdevelopment, and new features are available regularly. And although this tip focuses on how to use the ProSplign piece, if you haven’t used it much it will help you to understand how a number of tools within the Workbench can be accessed. You can also see that Splign is available in the tool list–which is another NCBI tool for a similar type of process, but with mRNA sequences as the focus.

If you want to have a text-based type of walk-through instead, there is a page that will take you through the features (see the quick links below). And there are other videos that will help you to explore the Genome Workbench features as well–there’s a handy special playlist of just those 视频. Subscribe to their YouTube channel for notices of their new items.


NCBI的基因工作台的: http://www.ncbi.nlm.nih.gov/tools/gbench/

Text-based tutorial page: https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial13/


卡普斯京, 华, Souvorov, 答:, Tatusova, 吨, & 李普曼, ð. (2008). Splign: algorithms for computing spliced alignments with identification of paralogs Biology Direct, 3 (1) 分类号: 10.1186/1745-6150-3-20

NCBI staff (2016). 国家生物技术信息中心的数据库资源 核酸研究, 44 (D1) 分类号: 10.1093/nar/gkv1290


一周的视频提示: JGI user meeting videos, and MetaSUB

Mason JGIThis week’s Video Tip of the Week is actually a whole bunch of videos. Although I’ll highlight one here as our tip, there are many great talks from the recent JGI Genomics of Energy & Environment meeting. Although typically we focus on specific software tools for our tips, I think this is a nice case of also looking at the type of research done with the tools.

This is a nice example of how to make a meeting accessible for a lot of people as well, using multiple strategies. 该 video channel, a Storify, dropboxes of slides (下面), 和 agenda details can help you to decide what might be relevant for your work. 例如, 我们已经谈论 泊坞窗, but you can now see how it’s deployed by the folks who are talking about it here. There’s a talk with Phytozome. And much more.

For today I’ll highlight MetaSub as one of the projects from the Mason lab. The Mason lab has participated in projects you probably heard about in the media–including swabbing the NYC subway system. You can see that data at PathoMap. MetaSUB stands for a data collection effort coming up soon, the Metagenomics & Metadesign of Subways and Urban Biomes. A global swabbing festival of the 10 busiest subways in the world (including my own–I wonder if I can do the station in my neighborhood?), to get more geospatial metagenomics maps, find antimicrobial resistance markers, and look for new biosynthetic gene clusters. It will be held on June 21, 2016–the summer solstice. It will tell us way more about our urban environments than we currently know. Maybe too much. But it’s a great idea, sure to reveal things we don’t know about our lived environment right now.

And here are the slides for the talk, as promised in the video. Mason tweets them:

He seriously did get through those 138 slides in 30 分钟. I was skeptical when I downloaded them before watching through them with the talk–but he really managed it. I was kind of out-of-breath just watching it.

He also talked about extreme environment sampling, 和 MetaPhlan2 和 HUMAnN2 分析, in a later segment. The whole thing is an excellent and breezy discussion of real-world genomics and a lot of appealing stories that the public would connect with. They are also doing educational outreach with a HTGAA course (How To Grow Almost Anything). There some really fun stuff with the Gowanus canal (严重), and so much opportunity just hanging around in our cities. 但也–what’s growing in space. They are working on space station mold. And astronauts–the NASA twins. They are also sending up a MinION (which they checked to see would work in microgravity–see paper below).

It was a very engaging talk. From an apparently very busy guy.



PathoMap: http://www.pathomap.org/

MetaSUB: http://www.metasub.org/


Afshinnekoo, 大肠杆菌, Meydan, 三, 乔杜里, 学, Jaroudi, 四, 博耶, 三, 伯恩斯坦, 全, Maritz, j的, Reeves, 四, Gandara, j的, Chhangawala, 学, Ahsanuddin, 学, Simmons, 答:, Nessel, 吨, Sundaresh, 二, Pereira, 大肠杆菌, 约根森, 大肠杆菌, Kolokotronis, 学, Kirchberger, 全, 加西亚, 一, Gandara, 四, Dhanraj, 学, Nawrin, 吨, Saletore, 华, 亚历山大, 全, Vijay, 体育, Hénaff, 大肠杆菌, Zumbo, 体育, 沃尔什, 米, O’Mullan, 克, Tighe, 学, 达德利, j的, Dunaif, 答:, Ennis, 学, O’Halloran, 大肠杆菌, Magalhaes, 吨, Boone, 二, 琼斯, 答:, Muth, 吨, Paolantonio, 光, Alter, 大肠杆菌, Schadt, 大肠杆菌, Garbarino, j的, Prill, 河, Carlton, j的, 征, 学, & 石匠, ç. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 1 (1), 72-87 分类号: 10.1016/j.cels.2015.01.001

Alexa B.R. McIntyre, Lindsay Rizzardi, Angela M Yu, Gail L. Rosen, Noah Alexander, Douglas J. Botkin, Kristen K. 约翰, Sarah L. Castro-Wallace, Aaron S. 伯顿, Andrew Feinberg, & Christopher E. 石匠 (2015). Nanopore Sequencing in Microgravity bioRxiv 分类号: 10.1101/032342