Good afternoon.
Welcome to the very short NCBI minute on alerts for new data.
As per usual, this recording as well as the slides will be available both in the YouTube
channel, the webinars playlist and on the FTP site.
You can find the links here.
I will give you a minute to copy the links down.
(https://go.usa.gov/xXqGG)
So over the next few minutes we will talk about setting up alerts for new data using
My NCBI.
I am Ben Busby, the bioinformatics training lead here at NCBI, and I have with me Peter
Cooper who is the head of the NCBI education group.
Many of you most likely use NCBI literature resources.
Many folks are very used to using My NCBI to do regular literature searches.
However many of our users do not know that you can also save searches for data.
For example, for new assemblies or annotations.
For new Geo data sets or new SRA data sets.
I will walk you through how to do that over the next few minutes.
The majority of you probably know that MyNCBI is simply a way to have an account at NCBI.
It's trivial to sign up for a MyNCBI account.
In fact, when I was preparing this webinar I signed up for a MyNCBI account.
Simply so I could have a fairly clean demonstration.
It's reasonably an easy thing to do.
There are many folks out there with MyNCBI accounts.
I encourage you to get one.
Creating alerts from any search string at NCBI is simple.
Really all one needs to do is click the create alert button below the search they are already
doing.
Say I was searching Geo for Alzheimer's and human.
You may only have one data series as shown here.
I can click the create alert button.
The alert dialog box would come on.
I can modify my search term and I can name my saved search.
I typically use the defaults but if you do a lot of these I could see that you want to
name them in a more systematic way.
You can either keep the filters or not.
There are a bunch of ways you can get email updates.
This is really quite simple to use and a lot of people have told us they would like to
see this service which in fact exists.
As I mentioned earlier, you can also get alerts for bacterial annotation and assemblies.
This is useful in my opinion, in the microbial realm.
For example, if I want to see new releases of Salmonella, either assemblies or annotations,
I can do this search in the NCBI Assembly database.
I believe, the NCBI Assembly database is a very clean and useful resource for finding
genome assemblies.
Also if you were to do SRA searches, for example for meta-genomes, you could do that.
The search I did here was for digestive decontamination.
It's a fascinating thing that is sometimes done to folks, patients in intensive care
units.
Here you can see a time course of such experiments.
Interestingly enough, you can blast into this time course to look into different bacterial
gene loci that return to the gut after this massive course of antibiotics.
I can save this search simply by clicking on the create alert icon.
Another nice thing that MyNCBI will do for you that many folks don't know about, is it
will save custom tracks.
Both track configurations that you can set up in the NCBI genome data viewer by clicking
on the Tracks button, but also data that you upload.
Here I uploaded a file called test.bed.
And MyNCBI will save that.
As with all of our resources, we have documentation.
You can get those from the NCBI Learn page.
If you Google for NCBI webinars, it is an easy way to find the webinars page.
My favorite way to get to this documentation page is to go to NCBI/learn and you will be
able to go to the documentation.
Once again, an updated version of these slides will appear on the FTP site in approximately
one hour from now.
Some of these links will be more simple.
Another thing I do in my position at NCBI is I run Hackathons.
We have a bunch of them coming up and if you are pretty familiar with Linux and can do
some basic scripting, if you are interested in bioinformatics or medical informatics,
you should consider coming to one.
These are the Hackathons that are coming up.
Some of them look very interesting and there are some shaping up for spring of 2018.
In my group I also have intensive internships for grad students, postdocs and clinicians.
You can come here to work for 4 to 6 weeks on either your project or ours, in a collaborative
environment and leverage NCBI resources.
We ask that you document the stumbling blocks that you run in to at NCBI.
If that is something you're interested, in please email bioinformatics-training@ncbi.nlm.nih.gov.
With that, what I want to do is take some questions, any questions you may have.
If there are questions that I do not know the answer to, we will either answer them
on the FTP site or Peter Cooper can answer them in person.
I see no questions in the question pod.
It's obviously a pretty simple and straightforward NCBI minute.
If there are any questions I will give you the next minute or so to type them in.
If not, I hope you all have a good day.
A fantastic rest of the week.
Thank you for coming to this NCBI webinar.
If you have feedback about the webinar, you would like to see more, or would like us to
dwell longer on a specific thing, please feel free to email webinars@ncbi.nlm.nih.gov or
put those comments right here in the questions pod.
Fantastic.
I don't see any questions.
Thank you to those who said thank you.
Like I said, I hope everyone has a fantastic week.
Good luck with your research or whatever else it is you do.