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.






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