A OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, So, 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.
Sempre, 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. Naturalmente, negli USA, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Sospiro.
Middleton, A., Mendes, Á., Benzoino, C. M., & Howard, H. C. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. Medicina Personalizzata, (14:3) , Pagine 249-257 , DOI 10.2217/pme-2017-0001.
Ok, 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 e SIFT, 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, M., Prüfer, K., Wagner, A., & Kelso, J. (2017). Functional implications of Neandertal introgression in modern humans Genome Biology 18:61. DOI: 10.1186/s13059-017-1181-7
This week’s video tip was prompted by a couple of things. Primo, it was a tweet from FlyBase, about their video channel. 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 (SGD) with a plea:
I 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, naturalmente. 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).
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 Natura e Scienza 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.
Lately I’ve been keeping an eye on a lot of the tools that link individuals with sequence data, loro fenotipi, and researchers/physicians who may either study or treat the associated medical issues (vedere 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.
Khalid, F., Aguilar-Rodríguez, J., Wagner, A., & Payne, J. (2016). Genonets server—a web server for the construction, analysis and visualization of genotype networks Nucleic Acids Research DOI: 10.1093/nar/gkw313
Il team di 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 ENCODE 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. Se non si ha familiarità con il Codifica i dati 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 speciale: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look.
Rivelazione: UCSC Genome Browser tutorials are freely available because UCSC sponsor us to do training and outreach on the UCSC Genome Browser.
Sperone, M., Ramo, A., Rosenbloom, K., Raney, B., Sponsor, B., Nejad, P., Sottovento, B., Imparato, K., Karolchik, D., Hinrichs, A., Heitner, S., Difficile, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barbiere, G., Haussler, D., Kuhn, R., & Kent, In. (2016). Il Browser UCSC Genome banca dati: 2016 aggiornamento Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275
Il progetto ENCODE Consorzio (2012). Un'enciclopedia integrata di elementi di DNA nel genoma umano Natura, 489 (7414), 57-74 DOI: 10.1038/nature11247
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, e così via. 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.
Il sito è 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.
C'è un “benvenuto” video that they’ve made, but it’s light on the software details. Ancora, anche se, 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, anche se, 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 (qui di seguito) that provide some further information about the project [Nota: il Genetica in Medicina one goes to a paywalled, pezzo–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.
Chong, J., Yu, J., Lorentzen, P., Parco, K., Jamal, S., Tabor, H., Rauch, A., Saenz, M., Boltshauser, E., Patterson, K., Nickerson, D., & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features Genetica in Medicina DOI: 10.1038/gim.2015.161
L' Alleanza globale per la Genomica e la salute (GA4GH) ha messo a punto un paio di volte sul nostro blog. L'ultima volta che li abbiamo evidenziato per una punta, Era circa il loro strumento di Beacon. L'idea del Beacon è che potrebbe interrogare un database, ma in modo molto sottile, senza dover accedere a tutta la sequenza di informazioni di un paziente. Sarebbe chiedere un semplice sì / no domanda su una data sequenza variante–e se un “sì” torna indietro, poi un ricercatore potrebbe passare attraverso il processo di ottenere un adeguato accesso ai dati del paziente protetti.
Quindi è stato un modo per impedire alla gente di scalpitare attraverso i dati che non hanno bisogno. E tuttavia potrebbe ancora connettere le persone che potrebbero trarre beneficio dalla ricerca, con i ricercatori che hanno bisogno di informazioni.
Ma certamente questioni di privacy del paziente o del donatore sono temi caldi. Sempre più dati saranno entrare in progetti di grandi dimensioni, o da campioni diagnostici, e il cancro vs normali confronti dei tessuti, e ci accingiamo a lottare con l'accesso vs. privacy conta per un po '. Il grande pubblico è solo ora diventando consapevoli degli impatti. Ma abbiamo certamente bisogno di persone a capire e noi vogliamo loro di contribuire ad ampliare le nostre conoscenze sulla salute e malattia.
Ecco perché le persone associate a GA4GH, il Wellcome Trust, e il Campus Wellcome Genome sono desiderosi di coinvolgere il pubblico sui loro sentimenti sull'uso dei dati sequenza genomica. Essi hanno lanciato un progetto chiamato “Il vostro DNA Dite la vostra”[PDF], sotto forma di un sondaggio con i video per aiutare a capire dove le persone sono su questo tema. Ecco il video introduttivo per invogliare a rispondere al sondaggio:
Ho risposto al sondaggio, perché io ho preoccupazioni per l'accesso alle informazioni che ci aiuteranno a guidare la scienza in avanti, così come circa il potenziale per uso improprio delle informazioni. Ma vorrei loro di sentire da quante più persone possibili, in modo che possiamo capire le barriere per la ricerca e la donazione che si profila. Dite la vostra. E diffondere la parola.
Si può imparare di più sulle loro idee in una varietà di pubblicazioni–Mi collego a quello qui sotto, ma ci sono altre pubblicazioni e maggiori dettagli sui progetti complessivi e singoli strumenti sul sito web GA4GH.
Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Bruciare, J., Calvo, F., Lacombe, D., Queste, B., Settentrionale, K., Sawyers, C., & , . (2015). Tutto il mondo è un palcoscenico: Facilitare Discovery Science e migliorata la cura del cancro attraverso l'Alleanza globale per la Genomica e la salute Cancer Discovery, 5 (11), 1133-1136 DOI: 10.1158/2159-8290.CD-15-0821
There are many tools at NCBI, with a huge range of functions. Letteratura, sequenza di dati, variazioni, struttura della proteina, chemicals and bioassays, e altro ancora. 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. Per questa settimana suggerimento della settimana, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.
Sebbene l' Genoma Workbench 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 video. Subscribe to their YouTube channel for notices of their new items.
This 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. L' video channel, a Storify, dropboxes of slides (qui di seguito), e il agenda details can help you to decide what might be relevant for your work. Per esempio, di cui abbiamo parlato Docker, 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 verbale. 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, e MetaPhlan2 e HUMAnN2 analisi, 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 (sul serio), and so much opportunity just hanging around in our cities. Ma anche–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, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E., Zumbo, P., Walsh, M., O’Mullan, G., Tighe, S., Dudley, J., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T., Boone, B., Jones, A., Muth, T., Paolantonio, K., Alter, E., Schadt, E., Garbarino, J., Prill, R., Carlton, J., Tributo, S., & Muratore, C. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 1 (1), 72-87 DOI: 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. Giovanni, Sarah L. Castro-Wallace, Aaron S. Burton, Andrew Feinberg, & Christopher E. Muratore (2015). Nanopore Sequencing in Microgravity bioRxiv DOI: 10.1101/032342