A TARGETED CURRICULUM DEVELOPED BY THE COMPUTATIONAL BIOLOGY DEPARTMENT
In accordance with a request in 2016 from the former General Board of Directors, the Computational Biology Department has developed this training program dedicated to Institut Pasteur PhD students. Each and every student at the institute must attend at least 50 hours of training. At the minimum, he or she is required to validate the statistical modules (which, depending on their background, some students may skip), and possibly choose additional modules according to his or her background and field of research.
A CORE FOUNDATION AND THE OPTION TO SPECIALIZE
This 50-hour training program required for all Institut Pasteur PhD students begins with a group of common core courses including a knowledge base in reproducible research, R Programming and Statistics. Each student then chooses a track of additional modules— Bioinformatics or Image Analysis—according to their background and field of research. Students already proficient in R programming and statistics can skip certain modules or the entire track.
This 6h course is mandatory for all PhD students. They will learn how to get help and assistance from the Department of Computational Biology and from the Hubs for questions in programming, experimental design, data analysis and image analysis. They will attend three short lectures in programming and reproducible resaerch. Finally, they will have the opportunity to assess their level in R programming and statistics and to register to the modules of their choice in the R programming and statistics, Bioinformatics and Image analysis tracks.
Program of the mandatory common core module
Other modules
The figure below shows all the available modules. To attend these lectures you need to bring your own laptop. No special configuration is required. Just avoid to come with your grandma’s machine.
To attend these lectures you need to bring your own laptop. No special configuration is required. Just avoid to come with your grandma’s machine.
Description of the Bioinformatics program
A detailed description of all modules can be found here.
To attend these lectures you need to bring your own laptop. No special configuration is required. Just avoid to come with your grandma’s machine.
SUPPORT
This PhD program is supported by the INCEPTION project.
There is a wide gap between the generation of large-scale biological data sets and more-detailed, structural and mechanistic studies. However, recent work that explicitly combine data from systems and structural biological approaches is having a profound effect on our ability to predict how mutations and small molecules affect atomic-level mechanisms, disrupt systems-level networks and ultimately lead to changes in organismal fitness. Our group aims to create a stronger bridge between these areas primarily using three types of data: genetic interactions, protein-protein interactions and post-translational modifications. Protein structural information helps to prioritize and functionally understand these large-scale datasets; conversely global, unbiasedly collected datasets helps inform the more mechanistic studies. Our efforts in this respect have been focused on three disease areas: cancer, infectious diseases and neuropsychiatric disorders. Our work has found remarkable similarities between these and other disease areas which are leading to novel therapeutic strategies.
Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting
Sustained malaria control over an eight-year period in Papua New Guinea: the challenge of low-density asymptomatic infections
Main speaker : , from Date : 23/09/2017 at
Location : ,Institut Pasteur, Paris
BACKGROUND:
The scale-up of effective malaria control in the last decade has resulted in a substantial decline in the incidence of clinical malaria in many countries. The effects on the proportions of asymptomatic and submicroscopic infections, and on transmission potential are yet poorly understood.
METHODS:
In Papua New Guinea, vector control has been intensified since 2008, and improved diagnosis and treatment introduced in 2012. Cross-sectional surveys were conducted in Madang Province in 2006 (n=1280), 2010 (n=2117) and 2014 (n=2516). Infections were quantified by highly sensitive qPCR and gametocytes by RT-qPCR.
RESULTS:
P. falciparum prevalence by qPCR decreased from 42% in 2006 to 9% in 2014. P. vivax prevalence decreased from 42% in 2006 to 13% in 2010, but then increased to 20% in 2014. Parasite densities decreased 5-fold from 2006 to 2010; 72% of P. falciparum and 87% of P. vivax infections were submicroscopic in 2014. Gametocyte density and positivity correlated closely with parasitemia, and population gametocyte prevalence decreased 3-fold for P. falciparum and 29% for P. vivax from 2010 to 2014.
CONCLUSIONS:
Sustained control has resulted in reduced transmission potential but an increasing proportion of gametocyte carriers are asymptomatic and submicroscopic and represent a challenge to malaria control.
Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting
Thursday 3rd of December, Pierre Neuvial will talk about performance evaluation of DNA copy number segmentation methods. #C3BIPasteur
EVENT : C3BI Seminars – Large audience
Performance evaluation of DNA copy number segmentation methods
Speaker : Pierre Neuvial, CNRS researcher from Laboratoire de Mathématiques et Modélisation d’Evry (LaMME) – Équipe Statistique & Génome – Université d’Evry Val d’EssonneTime : 02:00 pm Starting Date : 03/12/2015
Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris
A number of bioinformatic or biostatistical methods are available for segmenting DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these methods is generally assessed using unrealistic simulation studies, or based on small real data analyses.
In order to make an objective and reproducible performance assessment, we have designed and implemented a resampling-based framework to generate realistic DNA copy number profiles of cancer samples with known truth. In this talk, I will describe this framework and its application to a comparison study between methods for segmenting DNA copy number profiles from SNP microarrays.
This study indicates that no single method is uniformly better than all others. It also helps identifying pros and cons of the compared methods as a function of biologically informative parameters, such as the fraction of tumor cells in the sample and the proportion of heterozygous markers.
Reference:
M. Pierre-Jean, G. Rigaill and P. Neuvial
Performance evaluation of DNA copy number segmentation methods.
Briefings in Bioinformatics (2015)
http://bib.oxfordjournals.org/content/16/4/600
Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting
CDD en Bioinformatique au sein de la Cellule Informatique pour la Biologie
Le CIB (Cellule Informatique pour la Biologie) est une composante majeure du nouveau centre de Bioinformatique, de Biostatistiques et de Biologie intégrative (C3BI) de l’Institut Pasteur. Son rôle est de répondre aux besoins informatiques des scientifiques du campus par le développement, la mise à disposition et le déploiement d’outils bioinformatique.
Son pôle “Intégration Web et Développement Logiciel” recrute un Ingénieur (Bio-)Informatique dans le cadre d’un CDD (6 mois, du 01 novembre au 15 mai 2015).
→ Vous assurerez, en collaboration avec le reste de l’équipe de la plate-forme Galaxy de l’Institut Pasteur:
L’évolution de celle-ci (mises à jour, modifications de la configuration)
Le développement et la maintenance d’interfaces pour des outils bioinformatique
Le support et la formation aux utilisateurs
→ Vous participerez aussi à l’étude de faisabilité de la mise en place d’un serveur public Galaxy.
Compétences requises
De formation BAC+5, type Master Informatique/Bioinformatique, vous maitrisez le langage de programmation Python ainsi qu’au moins un logiciel de gestion de versions. Vous avez des connaissances des formats XML, JSON et de préférence, une première expérience de Galaxy.
Maîtrise de l’anglais (lu et écrit).
Esprit d’équipe, ouverture d’esprit et autonomie sont des qualités recherchées.
English version below
Support engineer for Galaxy at the CIB in the Institut Pasteur
The CIB (Informatics cell for Biology) is a major component of the new Institut Pasteur Center of Bioinformatics, Biostatistics and Integrative Biology. Its role is to fulfill the scientific computational needs of the campus with software implementation, bioinformatics software providing and/or their deployment.
Its group “Web Integration and Software Development group” is hiring an (Bio-)informatics engineer for a 6 month contract(from November 1st to May 15th 2015)
In collaboration with the rest of Institut Pasteur’s Galaxy Team, he will insure:
The evolution of our Galaxy instance (updates, configuration modifications, …)
The implementation and the maintenance of Galaxy tools
The support and training for Galaxy users
→ He will also participate in the study of the possibility to create a public Galaxy instance hosted in the Institut Pasteur.
The engineer has to be familiar with Python, as well as a versioning tool such as git, or svn, … He will have working knowledge of XML, Json formats. Previous experience on Galaxy is a plus.
An open mind, autonomy and teamwork skills are mandatory for this position.
Proficiency in written and spoken English as well as minimal notions of French (for support and training tasks) are required.
If interested, send your application to olivia.doppelt@pasteur.fr and herve.menager@pasteur.fr
Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walk?
Upcoming Events : C3BI Seminars – Methodological – 09/03/2015 at 02:00 pm in Retrovirus room – LWOFF (22)
Date : 09/03/2015 at 02:00 pm
Location : Retrovirus room – LWOFF (22)
Speakers/Trainers : Jean-Baptiste Masson, Visiting Scientist from Janelia Farm Research Campus, Ashburn, VA, USA
For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at c3bi-ask@pasteur.fr
Biomolecules Random Walks, Heterogeneities and Model Selection: What Information is accessible from experimental Biomolecules Random Walks?
The development during the last 20 years of single biomolecule tagging allows unprecedented access to single biomolecule dynamics. Trajectories are now space filling in 2D and densities in 3D are rapidly rising. Thus, large amount of random walks are now accessible. These random walks bear information on both the biomolecule dynamics and on the environment properties. One of the key questions is how to exploit these random walks to gain quantitative information on the biological processes taking place and the nature of these random walks.
Growing number of data being accessible multiple statistical hypothesis can be tested. Bayesian Inference [1] is a natural tool to handle multiple environment models, large amounts of data and multiple statistical hypothesis. We will discuss the use of Bayesian Inference to analyse single biomolecule trajectories[2–4], show various local models to describe biomolecule dynamics, methods to analyse multi-scale dynamics and describe transitions to anomalous dynamics [3]. We will also comment on out-of-equilibrium dynamics and stochastic integrals dilemma.
Furthermore, numerous estimators lack robustness regarding linking mistakes of the tracking algorithm. We will show how to remove tracking by efficiently sampling the biomolecules assignment graph between images. We will comment the various methods to perform these sampling and discuss the inference of multi-scale fields. We will show time evolving maps at the full cell scale using high density tagging.
We will discuss toxins receptor interactions with lipid platforms and Glycine Receptors dynamics at the full cell scale in both neurons and transfected Hela Cells. Finally, we will quickly introduce InferenceMAP a user-friendly software to analyse random walks trajectories.
[1] U. Von Toussaint. 2011. Bayesian inference in physics. Review of Modern Physics 83:943-999.
[2] El Beheiry, M., Dahan, M. and J.-B. Masson. 2015. InferenceMAP: Mapping of Single-Molecule Dynamics with Bayesian
Inference. Nature Methods (In Press).
[3] Masson, J.-B, Dionne, P., Salvatico, C., Renner, M., Specht, C. G. , Triller, A. and M. Dahan. 2014. Mapping the Energy and
Diffusion Landscapes of Membrane Proteins at the Cell Surface Using High-Density Single-Molecule Imaging and Bayesian Inference: Application to the Multiscale Dynamics of Glycine Receptors in the Neuronal Membrane. Biophysical Journal 106 (1), 74–83 .
[4] Masson,J.-B., Casanova, D. , Tu ̈rkcan, S., Voisinne, G., Popoff, M. R., Vergassola, M. and A. Alexandrou. 2009. Inferring Maps of Forces Inside Cell Membrane Microdomains. Physical Review Letters 102 (4), 048103.
@EnguerrandH will present @whathealthfr association @aiderpasteur Thursday 27th of August 2PM in Lwoff building
Upcoming Events : C3BI Seminars – !hacking@pasteur – 08/27/2015 at 02:00 pm in Retrovirus room – Lwoff building
Date : 08/27/2015 at 02:00 pm
Location : Retrovirus room – LWOFF (22)
Speakers : Enguerrand Habran, Co-founder & President of What Health Association
For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at c3bi-ask@pasteur.fr
What Health : Bring to the global health the key of its own digital revolution.
What Health is an independent association whose mission is to make emerge and support innovation in healthcare, in particular thanks to the potential of the new technologies. Our process is conceived to take innovation at source and bring the right environment for its growing, to allow its establishment in healthcare system. What Health fosters exchanges and the collaborative working between several universe to help them become players in innovation in healthcare system.
What Health approach is diverse:
• « Bottom-up », the innovation is coming from the ground and borne either by healthcare practitioners or by patients.
• Collaborative, each player of our community that is willing to contribute to improving healthcare system can provide his know-how and expertise.
• Global, What Health supports innovation from its emergence to implantation in the healthcare system.
• Supported, What Health is partner of major players in the healthcare system.
• Ethical, What Health supports all projects that can improve health.
The What Health process consists of several actions:
• The “Cafés”, a meeting and debate place
• The Innovation challenge, collaborative events that allow to prototype a solution and validate the proof of its concept;
• The Hub, support structure dedicated to the development and establishment of projects.
As a facilitator, What Health makes no claim to intellectual property emerging from events and other activities. That applies also for any actor and partner of What Health. Therefore, the ownership of a project belongs to the team that supports it.
Website :http://what-health.org
Every Tuesday from 10AM to 12PM in 26-06-06A room.
Despite summer vacation, we will welcome you for the Open Desk today from 10 AM till 12AM in room 26-06-06A ! We have coffee, air conditioning and great people to answer your bioinformatics/biostatistics questions!
Every Tuesday from 10AM to 12PM in 26-06-06A room.
Despite the hot weather and summer vacation, we will welcome you for the Open Desk today from 10 AM till 12AM in room 26-06-06A ! We have coffee, air conditioning and great people to answer your bioinformatics/biostatistics questions!
Upcoming Events : First Fiocruz-IP-USP Hands-on Course Bioinformatics and Biostatistics. 19-30th October 2015 in Ribeirão Preto, Brazil
Date : 19-30th October 2015
Location : Ribeirão Preto, Brazil
Speakers/Trainers : Institut Pasteur International Network (RIIP) and the University of Sao Paulo.
First Fiocruz-IP-USP Hands-on Course Bioinformatics and Biostatistics
The aim of this course is to provide students with theory and practical tools to analyze Next Generation Sequencing (NGS) data. The course is composed of a theory and practice lessons . In the first week theory sessions will cover the main kind of HTS analyses (re-sequencing and variant analysis, de-novo sequencing, transcriptomics, ChIP-Seq, metagenomics), in addition to some general bioinformatics tools and Biostatistics. The second week is dedicated to practice, in which the students work with their own data in small groups with a mentor that guides them. The practice week is designed so the course is of immediate use to each student. We expect the students to go back to their countries with the necessary knowledge to continue working on their own data. Lastly, this course will also promote interactions through bioinformatics between Fiocruz, the Institut Pasteur International Network (RIIP) and the University of Sao Paulo.
The course will take place from the 19-30th October in Ribeirão Preto, Brazil.
For more information and to apply visit: http://bioinformatics.fmrp.usp.br/curso2015/
