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Re: [science-iwg] Introducing myself

Dear all,

my name is Giovanni Pizzi and I am a researcher at EPFL, Lausanne, Switzerland, in the group of prof. Nicola Marzari.

I jump in because I’m one of the developers of AiiDA (yes, the website is www.aiida.net; and yes, it’s written in python).

I was supposed to write to this list a few days ago to introduce myself and AiiDA, but then I got delayed, and in the meantime Mario was faster than me ;-)

So, let’s remediate now:

AiiDA is a project jointly developed by EPFL and by the Bosch Research and Technology Center in Cambridge (MA, USA). 

 It is at the core of a Swiss 12-year project, MARVEL, involving 33 principal investigators across 11 Swiss Institutions (http://nccr-marvel.ch/en/project) and of the Horizon2020 European projects on Exascale computing in Material Science, MaX (http://www.max-center.eu).

We are directly involved in both projects, as well as the CSCS supercomputing center where Mario is working (and indeed we are directly collaborating with Mario, who was visiting us yesterday).

The aim of AiiDA is to provide an infrastructure for managing large computations on supercomputers as well as pre-post-processing steps, automatically storing all the data, simulations, their relationship and the full provenance in a database, ensuring reproducibility of simulations and allowing for efficient querying. 

At the same time, we aim at providing a flexible interface for users, easy to use from python without knowing how a database works: the user just works on his simulations through AiiDA, and everything gets transparently recorded.
Moreover, we provide a workflow engine tailored for researchers - this means that workflow steps are python functions, rather than static blocks, because in most cases the logic of the workflow cannot is very dynamic and the researchers need to ‘play’ with it during the research. However, under the hoods, AiiDA keeps track of the full stack of calling/caller functions for provenance.

The infrastructure is mainly used now by physicists/material scientists working with atomistic simulations, but the code is plugin-based so it can be interfaced with any code with a command-line interface and input/output files that can be processed using python.

I hope this short summary is already useful, you can find more information on the website, on the online docs http://aiida-core.readthedocs.org/en/stable/, or on the publication G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky, AiiDA: automated interactive infrastructure and database for computational science, Comp. Mat. Sci. 111, 218-230 (2016) http://www.sciencedirect.com/science/article/pii/S0927025615005820
(or here if you cannot access the PDF: http://arxiv.org/abs/1504.01163)

But if you need more details, just ask!

Best,
Giovanni



On 29 Apr 2016, at 18:12, UOMo <uomo@xxxxxxxxxxx> wrote:

Hi Mario,

Welcome. Nice to have you involved.
If AiiDA is the mentioned project, then most of it is written in Python.
Just spoke at a Smart Data/Big Data related event in Munich where Python was also a hot topic and described as particularly helpful for Data Science. I proposed a talk about Python and PyDev more in the DevOps and Automotive area (also held it on a CloudBees event this week) but for EclipseCon France it was considered "too exotic" or the Automotive industry a too small niche (another talk on eTrice by the project leads wasn't accepted either though it just went 1.0)

I am not in Switzerland right now after working there last year, but maybe there's an opportunity like an Eclipse DemoCamp in Zurich or elsewhere to meet you. Or Science tracks and Unconference days like in Toulouse or later this year in Ludwigsburg. With the rare occasion of an EclipseCon US talk a few years ago I mostly attend events in Europe. And those colleagues who lead eTrice mentioned, their observation was, the European events (ECE or ECF) keep growing while EclipseCon NA seems to attract a much smaller crowd than a few years ago (e.g. when I was there) so it's not surprising to see another participant from Central Europe.

Werner

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Today's Topics:

   1. Re: Introducing myself (Philip Wenig)
   2. Re: Introducing myself (Jay Jay Billings)
   3. Lab automation tooling (Christian Pontesegger)
   4. Re: Lab automation tooling (Jay Jay Billings)


----------------------------------------------------------------------

Message: 1
Date: Thu, 28 Apr 2016 19:19:12 +0200
From: Philip Wenig <philip.wenig@xxxxxxxxxxxxx>
To: science-iwg@xxxxxxxxxxx
Subject: Re: [science-iwg] Introducing myself
Message-ID: <57224610.9040609@xxxxxxxxxxxxx>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Mario,

you're welcome :-).

Is AiiDA this one?
http://www.aiida.net

It would be great if you could give us/me a short introduction to your
work on Taverna/KNIME and AiiDA.


Best,
Philip


Am 28.04.2016 um 13:55 schrieb Mario Valle:
> Hello enthusiasts!
>
> I just joined the mailing list. My name is Mario Valle and I work in
> the Swiss National Supercomputing Centre (CSCS) on Data Science issues.
>
> My exposure to scientific workflows dates many years ago, in the
> Bioinformatics area, trying to find my way around Taverna and KNIME.
> But at the end the project was simplified to a single tool so no
> workflow engine needed anymore. Than two years ago I had a shallow
> immersion in FireWorks to prepare an EU project proposal.
> Unfortunately the project had not been selected, but will be
> resubmitted next year hopefully with a more in depth understanding of
> workflow engines from my side. Currently I'm working with the AiiDA
> people to understand their workflow engine requirements.
>
> I'm sure the workflow manager landscape changed a lot lately and I
> want to explore it as best as possible.
>
> See you!
>             mario
>
>

--
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig ? Founder ? philip.wenig@xxxxxxxxxxxxx ? http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~



------------------------------

Message: 2
Date: Thu, 28 Apr 2016 13:42:45 -0400
From: Jay Jay Billings <jayjaybillings@xxxxxxxxx>
To: Science Industry Working Group <science-iwg@xxxxxxxxxxx>
Subject: Re: [science-iwg] Introducing myself
Message-ID:
        <CAE3ybv68VqyBWXGvnHAvAPzioUGCqh2KyAd80g6brsUe7Yso6Q@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="utf-8"

Welcome Mario! Great to get you involved!

There are quite a few workflow projects going on in the group, so let me
know if you have questions.

Jay
On Apr 28, 2016 7:55 AM, "Mario Valle" <mvalle@xxxxxxx> wrote:

> Hello enthusiasts!
>
> I just joined the mailing list. My name is Mario Valle and I work in the
> Swiss National Supercomputing Centre (CSCS) on Data Science issues.
>
> My exposure to scientific workflows dates many years ago, in the
> Bioinformatics area, trying to find my way around Taverna and KNIME. But at
> the end the project was simplified to a single tool so no workflow engine
> needed anymore. Than two years ago I had a shallow immersion in FireWorks
> to prepare an EU project proposal. Unfortunately the project had not been
> selected, but will be resubmitted next year hopefully with a more in depth
> understanding of workflow engines from my side. Currently I'm working with
> the AiiDA people to understand their workflow engine requirements.
>
> I'm sure the workflow manager landscape changed a lot lately and I want to
> explore it as best as possible.
>
> See you!
>                         mario
>
>
> --
> Ing. Mario Valle
> Swiss National Supercomputing Centre (CSCS)
> v. Trevano 131, 6900 Lugano, Switzerland
> Tel: +41 (91) 610.82.60
> _______________________________________________
> science-iwg mailing list
> science-iwg@xxxxxxxxxxx
> To change your delivery options, retrieve your password, or unsubscribe
> from this list, visit
> https://dev.eclipse.org/mailman/listinfo/science-iwg
>
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Message: 3
Date: Thu, 28 Apr 2016 20:17:12 +0200
From: Christian Pontesegger <christian.pontesegger@xxxxxx>
To: Science Industry Working Group <science-iwg@xxxxxxxxxxx>
Subject: [science-iwg] Lab automation tooling
Message-ID: <572253A8.9030403@xxxxxx>
Content-Type: text/plain; charset=utf-8; format=flowed

Hi,

while you know that I am doing scripting a lot, most scripts in our
company need to communicate with lab equipment (oscilloscopes, power
source units, waveform generators, ...). We are doing this using VISA,
IVI and typically National Instruments drivers. We are accessing all
this stuff from EASE scripts, using a self written intermediate layer in
C# to access hardware busses like GPIB. I am wondering how the other
science group members do this as I guess some of you will have similar
requirements. Are you all building your own stuff or is there a common
approach available already?

cheers
Christian


------------------------------

Message: 4
Date: Thu, 28 Apr 2016 17:15:03 -0400
From: Jay Jay Billings <jayjaybillings@xxxxxxxxx>
To: Science Industry Working Group <science-iwg@xxxxxxxxxxx>
Subject: Re: [science-iwg] Lab automation tooling
Message-ID:
        <CAE3ybv6D6E2N1FgiY4+C=2H=ijSvoVXq0qpim90q8WU6iX+nvg@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="utf-8"

Christian,

I think Matt Gerring (Diamond) or Kay Kasimir (ORNL) will likely have good
answers for you. Both are subscribed to the list.

Jay
On Apr 28, 2016 2:16 PM, "Christian Pontesegger" <
christian.pontesegger@xxxxxx> wrote:

> Hi,
>
> while you know that I am doing scripting a lot, most scripts in our
> company need to communicate with lab equipment (oscilloscopes, power source
> units, waveform generators, ...). We are doing this using VISA, IVI and
> typically National Instruments drivers. We are accessing all this stuff
> from EASE scripts, using a self written intermediate layer in C# to access
> hardware busses like GPIB. I am wondering how the other science group
> members do this as I guess some of you will have similar requirements. Are
> you all building your own stuff or is there a common approach available
> already?
>
> cheers
> Christian
> _______________________________________________
> science-iwg mailing list
> science-iwg@xxxxxxxxxxx
> To change your delivery options, retrieve your password, or unsubscribe
> from this list, visit
> https://dev.eclipse.org/mailman/listinfo/science-iwg
>
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