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Archives for November 2011

Structure Generation, Metabolite Space, and Metabolite Likeness

These are the slides of my talk “Structure Generation, Metabolite Space, and Metabolite Likeness” at the Unilever Center for Molecular Informatics in November 2011, Cambridge, UK. I presented these slides during my UK road tour in November 2011.


Structure Generation, Metabolite Space, and Metabolite Likeness


The chemoinformatics tools presented here are developed for metabolomics, specifically for metabolite identification. From our mass spectrometry experiments, and after data analysis, we want to identify certain metabolites of interest.

Of these molecules we might know the elemental composition (which and of how many atoms they are composed) and maybe one or more fragments (maybe a ring, a chain, or a functional group).

With this information we have to propose candidate structures for our unknowns. If we don’t find them in a database, we should generate the chemical structures with a computer tool, the structure generator.

Chemical Structure Generation

In this part of the talk I describe structure generator I have developed. It relies on the canonical augmentation approach proposed by Brendan McKay and it makes use of the Chemistry Development Kit (CDK).

The main use of this tool is: for a given elemental composition and prescribed non-overlaping fragment(s), it exhaustively produces all non-duplicate chemical structures.

Since the output list can be very large, we want to keep only those molecules that are likely to be metabolites. Therefore, we have developed a model that predicts the percentage of Metabolite Likeness of a molecule, this is, how likely a molecule is to be a metabolite.

Metabolite Space and Metabolite Likeness

We have combined 3 classifiers and 5 molecular representations to build metabolite likeness models. We wanted to see which combination could discriminate better metabolites from non metabolites.

The best models have been validated with a prospective validation set to asses that it can classify well new and unseen molecules.

We expect to use this model to rank candidate structures for unknown metabolites. Also, we hope these tools help scientist working in metabolite identification.


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Innovation According Best Chef, Ferran Adria

El Bulli y Ferran Adrià, la despedida 2010 502

Image by cronicagastronomia via Flickr

A cook talking about innovation, in general? Can you learn something from a food maker? Well, if it is Ferran Adrià who shares his wisdom you can learn more than in MIT. Nevertheless, Ferran Adrià has revolutionized how topnotch (and not so topnotch) restaurants prepare their food.

Adrià is the owner of El Bulli, the famous 3 Michelin star restaurant that has been awarded the World’s best restaurant distinction 5 times. Well, for sure he can talk about success. What about innovation?


80% of the innovation in the culinary world of the last 20 years came from “El Bulli”

Now were are talking!!

Recently Ferran Adrià shared his views on innovation at the 50th IESE’s Global Alumni Reunion. For him innovation should come from simplicity and not complex processes and big budgets.

Innovation According Ferran Adrià

  • Innovation does not require money, just ideas.
  • Innovation is easier than it seems … That’s what small and medium businesses do … Hustle!
  • Innovation is not a job: it’s a passion. You need ideas and to be bold.
  • It’s not a matter of money. I am tired of listening to people using money as an excuse.
  • We should teach our youth to be creative since early ages, but also teach them that budgets exist.
  • At work you should over deliver. This is how things are. You cannot look at the print of a contract and say: this is as far as I will go.
  • I am not Mother Teresa. At work I am demanding, I am tough … but I try to create a pleasant work environment.
  • I don’t know much about cooking, just a bit more than you. I am fed up of seeing so many knot-it-all experts.



This post was originally written in Spanish (La innovación según Ferran Adriá) by José Manuel Alarcón. He kindly allowed me to translate it and post it in my blog. Gracias José Manuel!

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Top 42 Books For PhD And Graduate Students

Little Book Worm (Canon G9)

From writing papers, to giving presentations, to grad school humor. These are the top 42 books for PhD and graduate students. If you want to survive in graduate school, you must read these books.

It is normal to feel lost in the vastness of a PhD project. Graduate school is a though place. You need to learn how to write, how to give presentations, how to do research, and how not to surrender.  And you have to learn fast.

Are you a graduate student that wants to know what (today’s) scientists had to do in order to finish at grad school? What they did to become good researchers? How come they didn’t go nuts in the process?

I expect this 42 books for PhD and graduate students to help in their quest for a career in science. Some of these books I have read myself or are in my to-read list. The remaining books have been recommended by very wise people that have survived and endured a PhD.

You will find all your answers in these books. If there is some missing gem, please let us know in the comments section.


Academic Writing Books

The Chicago Manual of Style, 16th Edition

A Manual for Writers of Research Papers, Theses, and Dissertations

How to Write a Better Thesis

Writing Your Dissertation in Fifteen Minutes a Day: A Guide to Starting, Revising, and Finishing Your Doctoral Thesis

The Literature Review: Six Steps to Success

Writing Your Journal Article in Twelve Weeks: A Guide to Academic Publishing Success

Merriam-Webster’s Collegiate Dictionary, 11th Edition

Dissertations And Theses from Start to Finish: Psychology And Related Fields

Academic Writing for Graduate Students, Second Edition: Essential Tasks and Skills

How to Write a Lot: A Practical Guide to Productive Academic Writing

On Writing Well, 30th Anniversary Edition: The Classic Guide to Writing Nonfiction


Presentation Skills Books

The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid

A Handbook of Public Speaking for Scientists and Engineers

The Visual Display of Quantitative Information

The Presentation Secrets of Steve Jobs: How to Be Insanely Great in Front of Any Audience

Even a Geek Can Speak

Presentation Zen: Simple Ideas on Presentation Design and Delivery

In The SpotLight, Overcome Your Fear of Public Speaking and Performing

slide:ology: The Art and Science of Creating Great Presentations

Confessions of a Public Speaker

Resonate: Present Visual Stories that Transform Audiences


Graduate School Motivation And General Advice Books

The Craft of Research, Third Edition

The Unwritten Rules of PhD Research

Mastering Your PhD: Survival and Success in the Doctoral Years and Beyond

A PhD Is Not Enough!: A Guide to Survival in Science

Advice for New Faculty Members

What They Didn’t Teach You in Graduate School: 199 Helpful Hints for Success in Your Academic Career

Getting What You Came For: The Smart Student’s Guide to Earning an M.A. or a Ph.D.

Advice for a Young Investigator

Surviving Your Stupid, Stupid Decision to Go to Grad School

Playing the Game: The Streetsmart Guide to Graduate School

Academics Handbook 2nd Ed

From Student to Scholar: A Candid Guide to Becoming a Professor

How to Survive Your PhD: The Insider’s Guide

The Smart Way to Your Ph.D.: 200 Secrets From 100 Graduates

Read This Before Our Next Meeting


Fun Comics

Piled Higher and Deeper: A Graduate Student Comic Strip Collection

Life is tough and then you graduate: The second Piled Higher and Deeper Comic Strip Collection

Scooped! The Third Piled Higher and Deeper Comic Strip Collection

Academic Stimulus Package (Piled Higher & Deeper)

xkcd: volume 0

5 Very Good Reasons to Punch a Dolphin in the Mouth (And Other Useful Guides)

I hope some of these books are useful for you. If you think other good books for PhD students should be included in this list, please leave a comment.

UPDATED: Check the Next Scientist

I have started a new blog to help PhD students and young scientist to do better science, get exposure and grow their academic footprint. All using digital hacks, blogging and social media. Check these blog posts, I think you might find them interesting:

3 Websites For Alternative Income Generation As A Scientist

3 Websites For Alternative Income Generation As A Scientist

Do you want to have an alternative income while working as a scientist?

Do you have some spare hours and you want to get extra bucks? Is your graduate scholarship not enough to pay for your lifestyle? Do you find exciting to work in different scientific and consulting projects in your free time?

The following websites will help you to sell your expertise and generate some alternative income as a scientist.


Innocentive is the meeting point for problem owners and problem solvers. You can change problems for “projects to be outsourced” and problem solvers by “smart scientists”.

A problem owner posts a challenge for which he is seeking assistance and provides a economical reward, which in many cases exceed 10K $ (not bad for alternative income). Some of these challenges require quite an effort and can should be performed in collaboration with other solvers.

Examples of challenges are: “Seeking Inhibitors of Fatty Acid Amide Hydrolase”, “How to Augment a Camera to Capture More than a Snapshot?”, or “The Cathode Ray Tube Challenge: New Uses for Recycled Glass”.


Acabiz is a similar concept to Innocentive.  This new website offers consulting opportunities to academic scientists within their field of specialization. Expect and alternative income per project in the range between 1K to 5K euros.

Currently, this new service has a large pool of knowledge holders, but not so many available contracts. Let’s hope that in the coming months we see an increase in the demand for experts.


Zintro is general marketplace in which science is not the main area of interest. Here you can find anything from lawyers, to accountants, to mathematicians, you name it. In this sense, it is not far form other generalist  freelance websites like or why you should consider Zintro?

If you check Freelancer or oDesk, the only scientific projects you can find fall in the category Scientific Writing. Fortunately, Zintro receives lots of project offers and best of all, you can describe yourself using a predefined set of keywords, which makes it easy to be found by potential seekers. As a matter of fact, I have been approached by people asking for advice in topics, which in many cases, were close to my expertise.


Room For Improvement In Freelancing Science

Truth be told, these websites still do not present a wealth of offers. Specially if you compare them with volume sites like or have.

I have discussed previously why scientists should consider freelancing as a valid career option. Unfortunately, these freelancing opportunities should come from other scientists and research companies, which might not be inclined to outsource their research projects.

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