I think you can continue to ask questions and we will give you some demos that gives you the
possibility to think of more questions. First out with a demo will be
Nikolay, please.
We're just talking about HPC and high performance computing facilitates
A couple of years ago, we had a big cluster, Abel and we had developed a web platform which
allowed users to use this cluster from a web interface, and this web platform was called Lifeportal
with Abel closing, we closed this platform too. Now with Fox emerging, we reinstall the same platform again.
So that the users can have access to a web interface, connecting them to the HPC facility. For those
who don't remember this, and I guess many of them knew, this platform is called Galaxy Fox.
It's a web platform or portal that allows the users to launch complicated jobs on a
high performance computing cluster, without having a deep knowledge about how people shall
write scripts and manipulate parameters for every computation. It provides web customized
menu for every tool, I can show it here on the the left hand side of the screen. For example, we
have a very simple box monitoring tool, which tells the users what the situation is, what the
status of the cluster is, how many free CPUs it has. How many jobs there are in the queue and
the tools below for genomics, for example BWA. the tools for BLAST. And in theory that these
tools which the user see in Fox, they are not here in Fox. These are the tools which run on
the cluster itself. Galaxy Fox, just provides a shell, or interface to the tools, which are
already installed on the high performance computing cluster. In addition you can upload data here with
upload file option and you can run the jobs. I can show just one of the jobs squeue.
Let's see how many jobs are running in the cluster, when the user can start running their own jobs.
We see here the number of the nodes, but all of these parameters are pre-selected. So if the users
don't know what they mean, they can just leave it as they are, they will be using the default ones
and click on execute.
The job is taken up by the Galaxy Fox portal sent to, you see here in the yellow window. The job is
running and it gets the results again in the same browser window, let me see how we can solve it.
Click on it.
I have this window for the eye, I don't see the eye because of the zoom. So we can see here...
The jobs which are running now and they're actually running, the status is R.
A more complicated menu of the tool is this, for example, I took NCBI BLAST on the left hand side. We see all
these parameters for the tool. These parameters are the same as the switches on the command line,
but they just skip this effort to the user. The user can just select from some dropdowns and of course, the prerequisite is that the user knows what the tool does in principle and puts the right parameters,
and the results will be appearing on the right hand side here where the green field is. In addition to this
The Galaxy Fox portal is based on Galaxy framework which is a very big community, built
initially for bioinformatics, but now it is being used for many other domains. They provide also
teaching tools and here in the nice small cap on the top.
You can see the Galaxy training materials, they vary from development and administration to a
simple user tasks, how you open a file, how you upload a file and so on. What is nice to say is that
actually being on the research Educloud it is within the same domain where
all the files of the unit are. So the problem of moving data from another source and bringing them into Galaxy Fox
Into the cluster box itself is so to say so. How does one get to this interface? If one types just Galaxy.Educloud.no
We get to this first page. There is a short description. Sorry, that was a reload
But when reloading, just a question from the side. Do you say that you need
Educloud projects to use these resources? Yes, that was what I was going to say
That the users need to have registered into a Educloud project before they run it.
They ask for access through this first page of the tool... Let's why it is not loading
properly today. Because the data is stored in Educloud? The data is stored in Educloud, Galaxy Fox
itself is installed in es. So it's basically the same physical location of the data
So, this is the first page of the service. As we have mentioned here before you start
you have to ask for access in this clicking Educloud window and people register here, they sign in
once they've signed in and this is
quite quick because we as administrators of the Galaxy Fox receive information that users have asked
for access. We just add them to the respective Galaxy Fox project and they can start logging it
and running the jobs from Galaxy Fox platform.
It uses a two-factor authentication.
We can try this to show
But you need... many users can share a project.
As long as the users are members of the project they can share the data, I mean, the project.
It's more complicated than this, in the sense that the Galaxy Fox runs the jobs
as one robot-user behind. So users don't have to know this, and they don't need to know this,
All the users within the Galaxy Fox, belong to the same project, but there are ways of grouping
the users inside Galaxy Fox, assigning them quotas, assigning project leaders
I mean inside this quad core. So you need access to this fox project? Yes, you need
access to that. I've written the first of this proxy, this is easy 73. Everybody shall log in and ask
because when one goes to Educloud anyway in the research Educloud interface, the first
step is to ask for access to apply for a project. So users can be members of many projects,
Normally one project of their own and one is e73, which will be the Galaxy Fox project. Once they've been added
to this project, they can use this web interface and they can select
the tool they want. What I forgot to say is that if the tool is not in the list, they can always
write to us. We provide here an email, it goes to the ticketing system, and they can always ask us to
add the respective tool to the list of the available tools. But as I said, the tools visible here are
a subset of all the tools which are available on Fox. So there is basically no
reason why we shall not make these tools available through this interface too
There is one more question, will this be available in TSD?
This is not solved yet, we haven't considered this yet. I think, if we ever try to do this in TSD,
we will have a dedicated platform for TSD, but it will not be a serious problem because everything is
automated, we have a complicated ansible playbooks for this. But can you say, do we have
any... What do we think about these categories data...
The black data and the red data. Can you use this system for that, health data?
As we see the data, it becomes red or yellow, or green just because we can see data like this
otherwise the data is always the same type. But as I said, there is no, even if it is a two Factor.
We still don't or cannot distinguish between red data or...
Yes, we get these questions every day on the data conference
What categories of data, what is allowed here and there... and I don't know, the lawyers said,
it depends. It will depend on us, what data locations will be available to this interface
There is another question here. Is there an equivalent Galaxy for HPC like hum or Betzy?
Not that I know of no.
Thank you very much. When you started this job in your demo
was that an R script? What kind of code...There must be some kind of code
to make this. In the example you showed, when you just started the
job. So these are two small tools we have developed for users to test. These are
very simple tools. And they run, there is a complicated machinery behind the scenes which run the jobs.
Prepare them in a specific format so it can be readable by all the queuing system on the cluster
and the cluster takes it in as any other regular job, run by user who is logged into the terminal
I think we can thank you Nikolay