Workshop on InfraOrange

Thanks to the collaboration with synchrotrons Elettra (Trieste) and Soleil (Paris), Orange is getting an add-on InfraOrange, with widgets for analysis of infrared spectra. Its primary users obviously come from these two institutions, hence we organized the first workshop for InfraOrange at one of them.

Some 20 participants spent the first day of the workshop in Trieste learning the basics of Orange and its use for data mining. With Janez at the helm and Marko assisting in the back, we traversed the standard list of visual and statistical techniques and a bit of unsupervised and supervised learning. The workshop was perhaps a bit unusual as most attendees were already quite familiar with these methods, but most haven’t yet used them in such an interactive fashion.

Marko explaining how to analyze spectral data with Orange.

 

On the second day Marko and Andrej took over and focused on the analysis of spectral data. We demonstrated the use of widgets specifically developed for infrared data and used them with data mining techniques we covered on the first day. After lunch the attendees tried to work on their own data sets, which was a real test for InfraOrange.

Orange for spectral data.

 

Group photo!

 

We now have a lot of realistic feedback on what to improve. There is a lot of work to do still, but a week after the workshop the most often occurring bugs have already been fixed.

The future of InfraOrange looks bright and…. khm… well, colorful! 🙂

The Story of Shadow and Orange

This is a long story. I remember when started my PhD in Italy. There I met a researcher and he said to me: »You should do some simulations on x-ray optics beamline.« »Yes, but how should I do that?« He gave me a big tape, it was 1986. I soon realized it was all code. But it was a code called Shadow.

I started to look at the code, to play with it, do some simulations… Soon my boss told me:

»You should do a simulation with asymmetric crystals for monochromators.«

»But asymmetric crystals are not foreseen in this code.«

»Yes, think about how to do it. You should contact Franco Cerrina, he’s the author of Shadow.«

I indeed contacted prof. Cerrina and at that time this was not easy, because there was no direct e-mail. What we had was called a digital deck net, Digital Computers Network. I had to go to another laboratory just to send him an e-mail. Soon, he replied: »Come to see me.« I managed to get some funding to go to the US and for the next two years I spent a good amount of time in Madison, Wisconsin.

I started to work with prof. Cerrina and it was thanks to my work on Shadow that I was called by the European Synchrotron Facility and they offered me a position. But soon I stopped working on Shadow, because I was getting busy with other things.

It was only in 2009 that I contacted prof. Cerrina again. We needed to upgrade our software, so I went back to the US two or three times and started working on what is now Shadow3.

 

In 2010 I organized a trip to go visit again with my family for the summer. We booked the house, we booked the trip… And it was ten days before the departure that I learned that Cerrina died. And since everything was already organized, we decided to visit the US anyway.

There, I went to Cerrina’s laboratory and met his PhD student, who was keeping his possessions. I said to her:

»Tell me everything you were doing recently and I will try to recover what I can.«

And at that moment, she said many things were on this big old Mac. So I proposed to buy this Mac from her, but my home institution wasn’t happy, they saw no reason to buy a second-hand Mac. Even though it contained some important things Cerrina was working on!

Luckily, I managed to get it and I was able to recover many things from it. Moreover, I kept maintaining the Shadow code, because it is a standard software in the community. At the very beginning, the source was not public. Then it was eventually published, but the code was very complicated and nobody managed to recompile that. Thus I decided to clean the code and finally we completed the new version of Shadow in 2011.

 

Three years ago it was time to update Shadow again, especially the interface. One day I discovered Orange and I thought ‘it looked nice’. In that exact time I met Luca [Rebuffi] in Trieste. He got so excited about Orange that his PhD project became redesigning Shadow’s interface with Orange! And now we have OASYS, which is an adaptation of Orange for optical physics. So I hope that in the future, we will have many more users and also many more developers helping us bring simple tools to the scientific community.

 

— Manuel Sanchez del Rio