Séminaire interne

Une fois par mois : du café, des croissants et un sujet de discussion.

22 juin 2018, 10:00 AM  (Room BAT5 02/022)   

Marc Chakiachvili, "Why and how to choose your IDE (integrated development environment)"

Résumé

 "An integrated development environment (IDE) is a software application that provides comprehensive facilities to computer
 programmers for software development. An IDE normally consists of
 a source code editor, build automation tools and a debugger. Most
 modern IDEs have intelligent code completion. Some IDEs contain a
 compiler, interpreter, or both. Sometimes a version control system
 are integrated. Many modern IDEs also have a class browser, an
 object browser, and a class hierarchy diagram, for use in
 object-oriented software development." 

 Well, that's only Wikipedia IDE definition....
 Clearly when developing complex pieces of software, use of an IDE
 can definitely simplify your programmer's life and reduce the time
 you spend developing...
    - So how and what should you consider before choosing the right
  IDE for your programs ?
   - Simple extensible Text Editor, or choose big and string IDE to
  ease your development ?
   - I'll show you the best ever IDE, everyone should use ! in my
  opinion, which is obviously unbiased !

14 juin 2018, 13:30 AM  (Room BAT5 02/022)   

Eric Rivals, "Hierarchical Overlap Graph"

Résumé

Given a set of finite words, the Overlap Graph (OG) is a complete
weighted digraph where each word is a node and where the weight of an
arc equals the length of the longest overlap of one word onto the
other (Overlap is an asymmetric notion). The OG serves to assemble DNA
fragments or to compute shortest superstrings which are a compressed
representation of the input. The OG requires a space is quadratic in
the number of words, which limits its scalability. The Hierarchical
Overlap Graph (HOG) is an alternative graph that also encodes all
maximal overlaps, but uses a space that is linear in the sum of the
lengths of the input words. We propose the first algorithm to build
the HOG in linear space for words of equal length.

28 avril 2018, 10:00 AM  (Room BAT5 02/022)   

Sylvain Pulicani, " Should we mine for Bitcoin in MAB ?"

Résumé

Nope! Want to know why? Come at this breakfast!

30 mars 2018, 10:00 AM  (Room BAT5 01/156)   

François Chevenet, "Phylogenies et Annotations : à la recherche de scenarios évolutifs. L'éditeur PAELA"

Résumé

Je présente le logiciel PAELA, dédié à l'analyse combinée de phylogénies et d'annotations (géographiques, résistances, etc.) pour l'aide à l'identification de scénarios évolutifs (resp.
phylogéographie, épidémiologie).

27 février 2018, 13:30 PM  (Room BAT5 01/156)   

Laurent Bréhélin, "Domaines de régulation vs. motifs de régulation."

Résumé

Je présenterai des travaux préliminaires qui visent à identifier des régions du génome montrant des compositions nucleotidiques qui semblent liées à un signal particulier (par exemple le niveau
d’expression des gènes auxquelles elles appartiennent).

15 février 2018, 10:00 AM  (Room BAT5 02/022)  

Denis Bourget, "Peer Community in : un système de recommandation public et gratuit de preprints"

Résumé

  Pour offrir une alternative au système actuel de publication - qui est notamment coûteux et peu transparent - nous avons initié le projet Peer Community in (PCI) - avec PCI Ecology, PCI Evol Biol,
    PCI Comput Stat. PCI repose sur la publication d’évaluations critiques et de recommandations d’articles non encore publiés, mais déposés – et gratuitement accessibles – sous forme électronique dans
    des archives ouvertes disponibles sur internet. Ces évaluations et recommandations sont réalisées bénévolement par les chercheurs sans aucun lien avec des éditeurs privés.
   
    Les frais de publication disparaissent : PCI offre la possibilité de valider, diffuser et consulter gratuitement les articles qui lui sont soumis. Les délais d’accès à l’information sont nuls : les
    articles scientifiques évalués sont déposés dans les archives ouvertes dès la fin de leur écriture. Le système devient transparent : les critiques, les décisions éditoriales, les réponses des
    auteurs et les recommandations sont publiées sur le site de la communauté scientifique concernée.

25 janvier 2018, 10:00 AM  (Room BAT5 01/156)   

Stéphane Guindon

14 décembre 2017, 10:00 AM  (Room BAT5 0/156)   

Alban Mancheron, "Comparaison de pipelines d'analyse de variants génomiques"

Résumé

Comparaison de pipelines d'analyse de variants génomiques

30 november 2017, 10:00 AM  (Room BAT5 02/156)   

Marie-Cécile Robert, "Presentation of the CRISPR/CAs9 system"

Résumé

 Marie-Cécile works in the MGC (Montpellier Genomic Collection) plateform of the IGMM. She will introduce us to the famous CRISPR/CAs9 system, its applications and why it is a revolution in molecular biology.

12 october 2017, 10:00 AM (Room BAT5 01/156)

Eric Rivals, "Presentation of the LIRMM survival toolkit"

Résumé

Je propose de présenter quelques outils pratiques pour la survie au LIRMM (mycore, gite.lirmm, filesender, ... et si j'ai le temps org mode).

22 june 2017, 10:00 AM (Room BAT5 2/022)

Marc Chakiachvili, "Why and how to choose your IDE (integrated development environment)"

Résumé

An integrated development environment (IDE) is a software application that provides comprehensive facilities to computer programmers for software development. An IDE normally consists of a source code
editor, build automation tools and a debugger. Most modern IDEs have intelligent code completion. Some IDEs contain a compiler, interpreter, or both. Sometimes a version control system are integrated.
Many modern IDEs also have a class browser, an object browser, and a class hierarchy diagram, for use in object-oriented software development."

Well, that's only Wikipedia IDE definition....

Clearly when developing complex pieces of software, use of an IDE can definitely simplify your programmer's life and reduce the time you spend developing...

- So how and what should you consider before choosing the right IDE for your programs ?
- Simple extensible Text Editor, or choose big and string IDE to ease your development ?
- I'll show you the best ever IDE, everyone should use ! in my opinion, which is obviously unbiased !

18 may 2017, 10:00 AM (Room BAT5 1/056 )

Emma Saulnier, "Zombie apocalypse and epidemiological modeling"

Résumé

A Zombie Apocalypse social media campaign by the US Centers for Disease Control and Prevention in May 2011 successfully raised awareness of hurricane domestic preparedness in an audience usually only
marginally receptive to public health messages, through comic-book graphic art and other underused media. We present technologies and applications related to zombie outbreaks modeling.
Les CDC américains ont mené en mai 2011 une campagne médiatique sur les réseaux sociaux intitulé "Zombie Apocalypse".
A travers une BD et d'autres média alternatifs, cette campagne a brillamment accrût la sensibilisation à la préparation aux tempêtes d'une partie de la population généralement peu réceptive aux
messages de santé publique. Nous présenterons ici les technologies et applications liées à la modélisation des épidémies zombie.

20 april 2017, 10:00 AM (Room: BAT5 01/124)

Krister Swenson, "Gluing computation experiments together with Snakemake"

Résumé

Do you have a program that operates on data produced by another program?
Snakemake is an efficient way to deal with interactions between a group of programs that depend on each other.
Some benefits of Snakemake are:
 1. python-based syntax (little syntax specific to snakemake)
 2. automatic parallelization of calls
 3. easily rerun only the necessary parts of an experiment after changes to code or input

I will present the basics of Snakemake and go through a simple example.

16 march 2017, 10:00 AM (Room: BAT5 02/022)

Rodrigo-antonio Canovas-barroso, "Debate about Compressed Structures"

Résumé

A compressed structure is a data structure modified to take up little space, besides providing direct access
and functionalities to answer certain queries on the stored data without need to decompress them.
Nowadays it has become of vitally important to operate on compressed data.
This is mainly because the information handled has grown exponentially and,
as an aggravating circumstance, secondary storage technology has not evolved enough in terms of speed.
Currently, main memory access is estimated at 10 ns, whereas disk access is estimated at 10^7 ns.
The speed difference is so vast that it is preferable to pay a moderate cost of access to a slower compressed structure,
that it fits in main memory, than to make constant access to disk.

In this context compressed structures make more sense, because by using a smaller space,
more information can be handled in main memory by paying a lower operating cost than
managing the same information efficiently on disk. However, still remains the question
for how long these structures will be still needed.

9 february 2016, 10:00 AM (Room: BAT5 02/022)

Clément Agret, "MARIANA: the cutest deep learning framework"

Résumé

VO :As neural nets increase in complexity they also become harder to write and harder to teach. Our hypothesis is that these difficulties stem from the absence of a language that elegantly describe
neural networks.
Mariana (named after the deepest place on earth, the Mariana trench) is an attempt to create such a language within python. That being said, you can also call it an Extendable Python Machine Learning
Framework build on top of Theano. VF :Plus les réseaux neuronaux augmentent en complexité, plus ils deviennent difficiles à écrire et à enseigner. L’hypothèse des développeurs de Mariana est que ces
difficultés proviennent de l'absence d'un langage qui décrit avec simplicité les réseaux de neurones.
Mariana (du nom de l'endroit le plus profond sur terre) est une tentative de créer un tel langage pour python. Cela étant dit, vous pouvez également l'appeler "Python Extensible Machine Learning
Framework" construite sur Theano.

8 december 2016, 10:00 AM (Room: BAT5 02/022)

Laurent bréhélin, "Cell biology by the numbers"

Résumé

"One of the central missions of our book is to serve as an entry point
that invites the reader to explore some of the key numbers of cell
biology. We imagine readers of all kinds with different approaches:
seasoned researchers who simply want to find the best values for some
number of interest or beginning biology students who wish to supplement
their introductory course materials. In the pages that follow, we
provide several dozen vignettes, each of which focuses on quantities
that help us think about sizes, concentrations, energies, rates,
information content and other key quantities that describe the living
world." http://book.bionumbers.org/

24 november 2016, 10:00 AM (Room: BAT5 01/124)

Fabio Pardi, "SIMONS human diversity project"

Résumé

The SIMONS project completed the 1000 human project by sequencing many
ancestral Asian and Oceania populations. Their results highlights the complexity
of ancestral Homo sapiens cross-breeding which occured at different times
and different continents (sapiens, neanderthalis and denisova).
A nice example of coalescence models application will be discussed.

20 october 2016, 10:00 AM (Room: BAT5 02/022)

Benjamin Linard, "Science and social networking"

Résumé

Social networks are more and more used by scientists to spread
their research (Twitter, LinkedIn, Facebook). But social networks specifically
targeted to scientists are now appearing (Google scholar, Researchgate).
Are these useful and can be considered as a research tool ?
Or are they just a consequence of the "mediatic science" in which we live
more and more, forgetting sometimes the purposes of science ?

Dernière mise à jour le 24/10/2018