Learning Neerlandese

Ik studeer graag nederlands, maar het is niet gemakkelik. Which means: I like to study flemish, but isn't easy.

Not at all.
Yes, I had my first dutch lesson today. Its hard, but not too much in fact. few rules, and lots of exceptions... Pronunciation is easy for italians, since only 'g' is pronounced a kind of guttural 'hgh'.

We'll see how I fare on the next les(sons)! for the moment GooieAvond.

Flops at the user group meeting

I've at the end, decided to decline the invitation to go up and speak at the next ChemAxon Users' Group Meeting.

It was enticing the idea of having been invited, although I do not hide to myself that they did so because they suddenly had one cancelation. Still, it's nice to know they thought of me.

But, I went for a decline. Too many things to do in the next few days, I did not feel like
adding one on top of the move, and most importantly the presentation in TiboTec. That one, could really get me a job. Plus, my mentor kind of suggested that I may get the opportunity of presenting my CV work, if she manages to avoid it. Finger crossed for bot. Now, that I would really like. Plus, it's certainly more scientifically interesting than showing a benchmark of badly performing softwares.

Hopefully, everything will coagulate nicely, in a big omelette which I will devour piece by piece in the next few weeks. Eggs, breadcrumbs, cheese, parsley and all the rest :-)

Just in case you were wandering who I work for, here it is: Janssen Pharmaceutica

Tops at the Box Office

	Shrek the Third
	Spider-Man 3
	28 Weeks Later
	Georgia Rule
	Disturbia

Here's a cut and paste of todays' tops at the box office from the IMDB

My Drug Development Training

Quite interesting training, yesterday...

A full day listening to the hypothetical structure of a drug development pipeline... from Discovery to Early Development, through the Clinical trials (I, IIa/b, IIIa/b), 'til Marketing and Post-Launch Follow-Up (often called Phase IV Trials).

Quite interesting, mostly for the comments of people who worked in one part or the other of said line... Noteworthy, a german guy who pointed out how actually very few, if any, drugs ever come out from the pipeline where expected, since often unexpected side effects open up new therapeutic possibilities for that molecules, and the original reason for developing it goes in the waste bin for one reason or another - extreme example is thalidomide, infamous drug retired from the market 'cause of its teratogenicity (is this the right word?) now enjoying a second life as therapy fornewly diagnosed multiple myeloma (don't ask me too much - check it on wikipedia).

I had my quibbles about the fact that the part on drug discovery and early development was presented, not explained, so that many of the non-technical people were left with doubts. What's the use iof just reading a definition of Half-life, or explaining what ADME means if then you don't explain what we actuially mean by the various ophases, particularly Distribution and Methabolism, the most esoteric for a non initiated? Yet, may be I am too harsh. I think I am not.

The last part, delivered by a marketeer, was very interesting, if a bit rushed out. I never thought that marketing did enter drug design since the very first phases o discovery, when they gently steer the research toward easily marketable and proficuous drugs. It certainly makes sense, just I never though of it.

That's it. food was good, and free, plus some ladies were worth looking at :-)

4th PostDoc Carnival.

The 4th PostDoc Carnival is up, at Minor Revisions this time.

This post pof mine (the most depressing of all) was selected...

Since when I posted that, situation has changed a bit, thankfully. With the thesis almost done, I have a better outlook to my future, although there still is a lot to do.

Papers from my PhD will have to be jotted down, following the outlines of the last two chapters - I do not consider the rest publishable - if not as a review - and that's already out there.

Then time will be up for my "in silico prediction of CV safety" paper, something very much on the map of pharma journals since quite some time - and the Vioxx affair only put it in the spotlight once again. I hope to provide a useful contribution there. plus, it's been fun, and it's helped me to get known within the company - I am going to lecture the sister company in the following days, and hopefully I'll fish a permanent position (I'm just moving in the same city, so that would help logistically too)

Finally, I've received a kind of direct invitation to go and present my latest work, a benchmark of pKa prediction softwares on our internal experimental database. The time frame for this is quite short though, I am not sure I will be able to make up a decent, nasty-question-proof presentation - no much stuff like this has ever been published and I understand why... every company has its own chemistry, and then, it isn't an easy job at all.

Every time I think about it, I would like to change something in the set-up. just revision hell, I would never be confident to put my name under a title such as "To pKa, or to not pKa? An extensive review and benchmark of current commercially available prediction software."

Ok, may be it would not sound that silly...

bah... we'll see what comes up next.

My presentation Training

I feel like JD in Scrubs today, with an inner voice following my own life, and frequent digressions in alternative realities...

Anyway, yesterday I had a very pleasant training experience: presentation skillz, something I felt I badly needed, although I have been definitely getting better in the past months (words of my bosses and mentors, not mine).

Still, the training was scheduled so there I went. nice to have patisserie in the morning as second breakfast...

and the talk was nice, delivered by a motherly south-african teacher with the kind of positive attitude everybody hopes to have when presenting his own story to an audience.

Not many tricks learned, in fact, more of general theory on how to grab but most importantly keep the attention of the spectators. It wasn't easy to follow, at times, since pretty girls were all around and I am easily distracted by cleavages (pig!)

At the end of the day, the moment most feared, an improvised presentation on a topic of our choice to the whole group, foloowed by real questions(!) and judgement on our style...

I was initially planning to present a tiny bit of my work, but then thought what the hell, everybody is going to do that and it would be boring, so I went for something completely different:

How (and why) to download movies and music form the internet (for free).

I actually insert two attention grabber right at the begin, back to back.

I first did ask "How many of you did ever download one mp3 from the internet?"

then I gave her a piece of (made-up, but realistic) statistic: 75% of the Internet Traffic is composed of peer-to-peer exchange (concept illustrated by a pie chart)

The whole lecture was structured following cartoons and hand-drawn (by me, yes) piccies, with me talking over them...

They did like,it, oh yeah... may be I'll get the chance to scan the piccie and post them up here...

Now I am off for another seminar, this time on the various processes of Drug Development...

See you soon!

Everybody stand back...

A different James Bond

Deinosuchus (aka Giant crocodile from the far past)

Quick, everybody go and look at Laelaps post on Deinosuchus.

Here's what wikipedia has to say about this big, big, big crocodile.

And here's what it shows:


Image below is drawn from the "Prehistoric Park" series, from Impossible Pictures - the place where Darren Naish now works. It's not deinosuchus but it was too juicy not to link it.

So, how's Shrek the Third?

Judging from the IMDB, the chicken isn't making golden eggs any more... I guess the character are getting tired and don't have that much to tell... here's what the NY Times has to say:

For all I know, there may be an endless supply of “Shrek” sequels in the pipeline. That DreamWorks ogre’s skin is the color of money after all. But there is nonetheless a feeling of finality about “Shrek the Third”, a sense that the tale has at last reached a state of completion. it goes on about the character reaching maturity and entering fatherhood, and so on...

Still, the popular vote is clear, with imdb scores decreasing from 8 (Shrek 100K+ votes) to 7.7 (Shrek II - 50k+) to 6.9 (3k+). Even accounting for the fact that early viewers may be hard core fans, and therefore harsher judges... the drop is severe and I don't think it will be recovered. Quite simply, the franchise has lost its allure. Even the fact that less people bothered to vote for the second is witness to this.

Well, as usual I doubt I will have time to go and see it in the theater, hence I will wait for a decent dvd rip to pop up on the net (ever heard of aXXo?) - and enjoy one of those boring fall afternoons.


See ya!

Light Blogging today

I am full-time into a seminar on how to improve my presentation skiilz.

Tomorrow, same thing, I'll have to attend one on the general layout of drug development: hopefully it will be general and not tied too much to my company only. Well, not 'mine', the one I work for.

fter that it will be ablur to reach the end of the week with some work done and some stuff already packed in the house before the big three-days move experience. Gawrsh!!!

Evangelion!!! Live Action!!!

The greatest of Gainax successes becomes a live action movie.

I just hope they get the chance to properly do the effects, as the one shown in this trailer do suck a little.

update: new trailer: it sucks even more. they didn't even get the taglines right. "A boy has to decideD" "The destiny of THE Humanity", oh yeah, that would be Humankind... never mind - have a look yourself.



And what's with the freaking american accent of Kusanagi? I hate Americans for being so self-centric (not that japs aren't when they set all the ultimate fortresses of humanity in their own little island (less than 1% of Erath surface, yet statistically unlucky to incredible levels.

AND - apparently is an easter egg. or fan art. in the case, they did a decent job.

Wings of Honneamise

First movie of Gainax. A very realistic telling of a space program in an alternative reality.

Slow, yet one of my favourite anime

Explosions

Some of the best explosion scenes froma collection of anime - I recognise most of the m - how geek am I?

New Piccie of the Month

Look at your right! I changed in advance the piccie of the month. as a bonus, and because I am not sure I will have that much time to post around in the following days, with all the busy things. seminars at work, move to mechelen and such.

Anyway, here is the elephant rock, a natural monument of my beautiful island. carved by wind and... more wind, I'd guess. actually, I don't think so, as it isn't smooth as wind-carved rock usually are.

You can find it here: It's the little dark spot at the center of the picture, just outside the road.

In the picture, you can also see my dear lady stretching up to reach the rock... almost there, but not quite. ;-)

And I'd believe it too!

I mean, I would believe it if the guy in black were to specify that the Space God was nothing less than the "Flying Spaghetti Monster"



Of course, the two turtles were hurled down, slammed together, their feet jammed, and voila`, here's planet Earth! Spherical as observed experimentally.

Why would you want your doctor to have studied evolution?

the 4 best answers are here.

and, from here, congrats to Gregory Simonian for winning!!!

MOE's LigPlot gizMOE rules!!!

I just tried to use MOE (Molecular Operating Environment) to draw a ligand/protein interaction diagram. I fell in love with these kind of graphs the first time I saw them, from the original LigPlot software. I love the way they represent the fundamental interactions without the fuss of 3D structures. I did once suggested the use of them rather than confusing 3D structs as output of a distributed docking program at my previous university. Look at the picture above, and it shows how a given ligand interacts with neighboring residues by means of hydrophobic contacts (the small sun-like drawings) or hydrogen bonds (the green line with distances)

Anyway, right now I just needed a couple of shots showing how the lipocalins' binding pockets are devoid of h-bond anchor points, if compared to other classes. Unfortunately, LigPlot for windows does not come without the hassle of having to mail his author, so I had to wait until I got back to work. Where we have MOE and their own implementation of the cake.

This morning, then, I loaded up three Lipocalins structures, plus one Exopeptidase, one Protease, and one Oxido-Reductase for comparison and hey!, presto, I have six wonderful shots lending weight to my assertion.


(picture here isnone of them, just a snapshot from MOE's website - again, green lines show h-bonds (without distance, but they have directionality as added bonus) - the green balls are apolar residues in hydrophobic contact.) I am not sure what the blue line is. Oh, there it is: When the hydrogen bond is formed with the residue sidechain, the arrow is drawn in green. Hydrogen bonds to the residue backbone are drawn in blue, with an additional dot drawn at the residue attachment point.
I just wish my current work was more structure-based to be able to play some more with all these cool softwares. Well, may be my next job? or life? who knows?

Plan for the week.

Finish off thesis.

Work on CV paper.

Look at In Vivo Clearance data.

Blog roll if I get a chance.

read up on xkcd the new (for me) webcomic I just discovered:



Solve this damn riddle...

Oh, I also have to catch up on Freefall and PennyArcade, if I get a(nother) chance.

Like Old Yoda my computer wants me to write

sneak peek at my PhD thesis (almost ready - now you know why I haven't posted the last four days) where Word's ortographic corrector suggest me some rather strange re-arrangement... I thought about writing all the post with inverse syntax but have not time right now... got to finish it. yet, I can't let it go... One last check... one last-minute addition... will I ever get rid of it? Stay tuned!