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Archives for December 2011

Understanding And Classifying Metabolite Space And Metabolite-Likeness

I have recently published a paper in PLoS ONE titled Understanding and Classifying Metabolite Space and Metabolite-Likeness.

Understanding and Classifying Metabolite Space and Metabolite-Likeness. 2011, PLoS ONE
Julio E. Peironcely, Theo Reijmers, Leon Coulier, Andreas Bender and Thomas Hankemeier.



Short Descritption Of The Paper

We have studied the chemical space of human metabolites.

We have built a computational model that assigns a metabolite-likeness score to input molecules.

We have studied which physicochemical properties and moieties are characteristic of human metabolites.

Long Description Of The Paper

This work describes the application of computational tools to predict the metabolite-likeness score of a molecule, i.e. how much it resembles a metabolite, and to acquire a global understanding of how the space of human metabolites is organized. In order to achieve this we made use of the state of the art in machine learning and the most comprehensive collection of human metabolites. To our understanding, we are the first to provide a metabolite-likeness score and to elaborate on its use for metabolomics, specifically in metabolite identification.

The use of computational models to classify metabolites and to compare them to other families of compounds has previously been published, but no prospectively validated papers have appeared.  The major contribution of the current work is threefold:

  1. We employ and validate a variety of computational methods to not only predict if a molecule is a metabolite or not, but also to assign a metabolite-likeness score to molecules.
  2. Three prospective validation sets are used to demonstrate the generalizability of our models and their applicability for drug research and metabolomics.
  3. We investigate which physicochemical properties and chemical moieties are characteristic of the metabolite space.

We believe that our work would be of interest to medicinal chemists performing drug research, but specially to scientists in the field of metabolomics. Our aim is to show the metabolomics community how they can benefit from chemoinformatics.

Therefore, we devise further development and application of this work to accelerate discoveries concerning metabolite identification.

Calculate Metabolite-Likeness Of Your Molecules

If you would like to calculate the Metabolite-Likeness of some molecules, please contact me ( peyron #at#

Ditto if you want to know more about this work or to collaborate with me.

The Warren Buffett Way To Improve Yourself

Warren Buffett speaking to a group of students...

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We all want to be somebody different. We all look up to someone we would like to imitate. There is so many people, me included, that feel inadequate, not good enough.

All what we want is to be better, improve ourselves. No wonder why self-help books abound in the New York Times’ list of Best Sellers.

The truth is that very few of us do something about it.

But what could be do? Can we just change ourselves automagically?

Well you can improve yourself if you want it really badly, if you feel enough pain.

It all starts by knowing what we want to change, what is it that we want to improve. There are lots of personality traits to work on and we need to focus. Focus. Focus. Focus.

It is not precise enough to say I want to acquire more good qualities and get rid of my imperfection. The key is to know what we want to acquire.

You need to define good and bad personality traits. And Warren Buffett has a great and simple (I love simple solutions) way of figuring out who you want to be.

As an example imagine you want to be more likable. This is, that people want to be around you, that they talk positively about you when you are not there. You want other to associate with you. This is to be a likable person.

Take 5 of your friends or people you deeply admire and describe what is the most prominent personality trait that you like about them. Is it that they listen well? Maybe they think first how to help you instead of their self interest? Are they positive in most situations? Why is it that you feel good when you are close to these people?

Write down their qualities of the people you like. This is what you want to acquire to be more likable.

Now take people you dislike, those that you have a bad gut feeling, those that you don’t want to hang out or make business with. Why is it that you don’t like this people? They don’t keep their promises? Do they look down on others? Are they energy suckers? Do they never speak up their mind? are they trying to be friends with everybody, thus making you not to feel special?

Write down the traits of those you dislike. This is what you want to get rid of to be more likable.

 It’s like switching your to-do and not-to-do lists, for a to-be and not-to-be list.

If you exercise enough the good personality traits, and remove the negative ones, you will turn into a much more likable person. 



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Kill Procrastination Guilt With The Pomodoro Technique

Italiano: Autore: Francesco Cirillo rilasciata...

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Being quite a procrastinator and a time wasting guy is not easy. Many times I feel guilty for wasting my time and my employers money. At least it looks to me I am wasting them. This procrastination guilt kept piling up day after day and the feeling was not a nice one.

When the end of the working days arrives, everything left is a bitter taste in my mouth that reminds me “I didn’t do enough today”. But even having so many unproductive days my bosses think I am still being productive.

How can this be? Are they using a different measurement?

Maybe just quantifying the amount of guilt I had after a day was not a good way to assessing my productivity. Since I tend to be quite hard with myself, perhaps I was doing a bit better than I thought.

Then it came to me, I should have my own way of measuring what a satisfactory day was. I didn’t want to lie to myself and not to base my satisfaction on other people’s opinion.

Basically I wanted two know:

I needed a way to answer two questions:

Has my day been productive enough? 

  • So I don’t need to feel guilty.

Have I been so far today productive enough?

  • So I can go home or start wasting my time guilt free.

And I found the pomodoro technique.

The Pomodoro Technique

  • Work uninterruptedly and hyper focused for chunks of 25 minutes (pomodoros). If somebody/something interrupts restart the pomodoro,
  • Take 5 minutes breaks between pomodoros and a 25 minute break after 4 pomodoros.

My goal was not to do a lot of pomodoros, but just to do enough pomodoros to be satisfied.

How To Get Rid Of Procrastination Guilt

  • Spend 2 or 3 days using the pomodoro technique and working hard.
  • Count the number (P) of pomodoros of each satisfactory day.
  • Try every day to finish P pomodoros, at least.

In my case 6 pomodoros is the minimum to not call it a wasted day. On the upper side, 8 or 9 pomodoros equate to a satisfactory day. 10 or more is a ballpark day. What is your ideal number of pomodoros?

Now when I start late my working day I know how many pomodoros I need to compensate in order to be happy.

The pomodoro technique is also useful if I want to spend part of my time on side projects, I make sure I have finished 6 or 7 pomodoros before hand. Then I can move onto something else guilt-free. It is that simple.

Now I cannot fool or punish myself anymore. And sometimes I surprise myself being more productive than expected.