• Climb up the Tree
  • Research
  • Evolution
Carry out real, original, and relevant research.
Join the research pilot program for high school.
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Pilot Program
“Climb up the Tree” Pilot Program FAQ
WHY PARTICIPATE IN THE PILOT PROGRAM?

PhylomeDB is a very powerful tool that can be used to carry out real, original, thorough, extensive, and relevant research. It is essential to understand how this tool works in order to carry out the research. But it is also necessary to establish a research goal. This implies deciding which proteins to use and what information to analyze.

The tool is free to use, but we recommend you participate in the pilot program we’ve organized for the 2016-2017 school year. During the pilot program, the CRG researchers behind PhylomeDB will offer advice on establishing the research goal and on how to use the tool.

HOW DOES THE PILOT PROGRAM WORK?

Once the registration process is completed, the organization will pick the candidates who meet the selection criteria.

Participants will meet in a face-to-face workshop on November 21st, 2016. During the workshop, we will go over how to use the tool. Some of its possible applications in the classroom will also be discussed. In this work session, teachers, researchers, and the experts at Eduscopi will collaboratively come up with possible ideas for the research papers.

Teachers will think the research papers through with their students and will then be given additional advice on research goals.

All research papers will be evaluated at the end of the pilot program, and one of them will win a prize: a summer stay in a CRG laboratory.

WHO CAN REGISTER?

High School teachers (from schools in Catalonia) who conduct research papers.

Limited capacity (a maximum of 15 participants).

Participants will be selected according to their interest and their previous experience in other innovative projects.

HOW CAN I REGISTER?

Registration will be online (via web form).

The registration deadline is October 31st, 2016.

WHAT ARE THE BENEFITS FOR ME?

Training on how to use the tool.

Advice from CRG researchers on establishing research goals.

The possibility of winning a prize to the best research paper (the author of the winning paper will win a summer stay at a CRG lab).

WHAT ARE THE PARTICIPATION COMMITMENTS?

To conduct (at least) one research paper which uses PhylomeDB.

To participate in the first workshop.

To share the goal of the research paper with the organization.

To fill out the follow-up forms sent by the organization.

Calendar

31/10/2016: End of registration period

21/11/2016: Initial workshop

February 2017: Personalized follow-up meetings

March 2017: Follow-up forms

June 2017: Research paper or progress report deadline

Last week of June 2017: Winner selection

Registration is now closed
Thanks to the 50 people who registered.
We appreciate your trust.
PhylomeDB
The research papers written during this pilot program will use the PhylomeDB tool.



What is it?
It’s a database that includes public and open information on the evolutionary relationship between a vast amount of proteins of different species.

More specifically, it’s a database that stores phylogenetic trees. These trees represent the evolutionary history of a family of genes that codify proteins. The database is organized into “phylomes”, which are complete collections of the evolutionary histories of all the genes in an organism and in its kin from other species.

What can I do with it?
When you search a protein in PhylomeDB, you obtain a representation of the evolutionary relationships between this protein and its homologs in other species.

This relationship is reflected in an interactive tree containing a vast amount of information that you can access with a single click.


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Why use it in a research paper?
PhylomeDB is an excellent starting point to carry out new research based on the use of open and public tools.

The vast amount of information included in and generated by this tool can spur real and original research.

The data has been automatically generated and analyzed as part of global studies, but most phylogenetic trees found in PhylomeDB have never been examined manually. Hence, it is a gold mine in which you can observe and discover things that remain unseen, yet may be clearly visible to a trained eye. In this web page you will find a user guide that provides training on how to explore this data. Also, by participating in the pilot program you can attend a workshop on how to use the tool and much more.

What kind of research can I conduct?
The search of a specific protein’s existing phylogenetic relationships can be the basis for further research. You can try to answer different questions, such as:
Example 1
Does the tree that traces relationships between proteins correspond to a possible evolutionary tree of the species within it?
What is the most evolutionarily distant species in which a homolog of this protein is present?
What is the role of the protein in two evolutionarily distant species?
Is its function preserved?
Example 2
If you compare the trees of two proteins, one with a function essential to survival and cell division and another one with non-essential functions, do you see any differences in the changes accumulated between them?
Can they be quantified?
Where do most significant changes appear?
Example 3
Are there proteins which have changed more rapidly or slowly in an organism (or a few organisms) in relation to the rest?
What implications can this have for its biology?
Example 4
Are there any signs that a gene has “leaped” from one species to another evolutionarily distant one?
Example 5
Are there any related organisms in which this protein has been lost?
If so, is the corresponding function carried out by a different protein or is the organism completely incapable of carrying it out?
What could be the evolutionary reason behind this loss?
Example 6
Do the homologous proteins in different species include the conserved domains identified?
If there are significant differences, is this reflected in the function of these proteins in these species?
Is there any research on the subject?
Example 7
Has any duplication event occurred during the evolutionary history of this protein?
What functions do the proteins derived from this duplication carry out?
Are there any changes in the protein’s function before and after the duplication?
Can a family of related proteins be established?
Example 8
You can explore the history of a specific gene that carries out an important function that you’re familiar with. Or think of evolutionary changes that must be reflected in the history of the genes.
For example, primates can see more colors than most mammals.
Do you see any evolutionary changes in the photoreceptor proteins we use to see colors?
PhylomeDB Guide
Learn more about how to use this tool with the guide put together for this pilot program.

You can also download the workshop exercises.

Go to the guide
Organization
Who organizes this pilot program?
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CRG

  • Toni Gabaldón Estevan
  • Laia Carreté Muñoz
  • Marina Marcet-Houben
  • Cinta Pegueroles Queralt
  • Irene Julca Chávez
  • Veronica De Pinho
  • Salvador Capella Gutiérrez
  • Miguel Angel Naranjo Ortiz

Eduscopi

  • Salva Ferré Benedicto
  • Toni Pou
Contact
For the time being, you can contact the organization at:
pujaalarbre@eduscopi.com