BIological networks, RaDiotherapy and Structures
Proton therapy is a type of external radiation therapy based on proton beams. The main benefit of this technique lies on the following proton property : protons of a given energy share a predictable common penetration distance in the patient (no proton penetrates further this distance). This property induces that the patient does not have to be irradiated on the complete path of the beam (which is the case for photons). Moreover, unlike photon therapy, the dose delivered to the tissues is maximal only on the last milimeters of this penetration distance (called Bragg peak). The position of the Bragg peak depends on the energy to which the particles have been accelerated by the proton accelerator. These dosimetric benefits are greatly degraded due to, on one hand, the cost and size of the neccessary equipments and, on other hand, to patient motions (e.g. breathing, heart beats) and physical variability (e.g. gain/loss of weights). The main goal of this project is to provide a software highlighting the impact of patient motions during a treatment. In addition, this tool is intended to be used to develop and propose new motion mitigation strategies based on the adjustment of the beam’s weight when the proton beam is scanning across the tumor.
We developed an ”open-source” software (GNU GPL v3 Licence) called MSPT (”Motion Simulator for Proton Therapy”). The main objective of this tool is to render the impact of patient motion and provide a tool to compare treatment plan or mitigation techniques to improve the treatment robustness to predectible motion such as breathing, heart beats, hiccup, cough. MSPT was developed in Python 2.7, for the flexibility of this programming language and using subroutines encoded in C to improve the execution speed of critical parts. MSPT deals with data in DICOM format (Digital Imaging and Communication in Medicine): patient CT image (Computed Tomography), the treatment plan (energies, beam positions, weights), the contour of the structures (e.g., entire patient body, organs, tumor), and optionally, the dose calculated by another TPS. Given a description of patient movement, MSPT provides an evaluation of the treatment plan quality.
During the PhD thesis of Paul Morel which was defended on November 17th at UPEM, we developped an open-source research tool named « Motion Simulator for Proton Therapy ». MSPT aims at highlighting the impact of the patient motion during a treatment delivery by computing dose on the moving patient. The main interest of this simulator lies in the ability to render the impact of a predicted patient motion on a prescribed treatment plan. This capability makes it an innovative research tool to evaluate and compare different methods of motion management or mitigation.
This project ended up in the establishment of a first essential brick of a broader project aiming at providing motion compensation solutions for proton therapy which is nowadays the main research field of Guillaume Blin who recently joined the LaBRI as a full professor. Further collaborations have been established with Institut Bergonié from Bordeaux and some Physicians of CELIA and CENBG and are now conducted under an Aquitaine Region project called POPRA.
This project ended up in the establishment of a first essential brick of a broader project aiming at providing motion compensation solutions for proton therapy. This last is an open-source software (http://code.google.com/p/mspt). This software is the subject of an article submitted to the journal «Technology in Cancer Research & Treatment«. Details of the work that led to this software are available in Paul Morel’s PhD manuscript (Paul Morel. MSPT : Motion Simulator for Proton Therapy. Computer Science. Université Paris-Est, 2014. English. <tel-01112637>)
The present project will take place in the AlgoB
(Algorithmic for Bioinformatic) group
(part of the Algorithmic team) of the Institut
Gaspard Monge, Université Paris-Est Marne-la-Vallée.
It is composed of the following members:
Guillaume Blin (Assistant professor, Université Paris-Est);
Maxime Crochemore (Emerit Researcher, Université Paris-Est and
Isabelle Fagnot (Assistant professor, Université Paris-Est and
Université Paris 7),
Sylvain Guillemot (Postdoc, Université Paris-Est),
Florian Sikora (PhD student, Université Paris-Est), and
Stéphane Vialette (group leader, CR CNRS, Université Paris-Est).
Research in the AlgoB team includes
the design of algorithms for the interpretation, classification and
understanding of biological datasets (RNA and protein-protein
interaction networks) and algorithmic issues of comparative genomics.
Computational biology has a long tradition in Marne-la-Vallée as it
started as early as mid-90 with Marie-France Sagot and Maxime
However, with the departure of Marie-France Sagot and
the emeritus status of Maxime Crochemore,
the lab needs to rebuild a new computational biology team.
Guillaume Blin has been recruited as an assistant professor in 2006
and Stéphane Vialette came as a CR1 CNRS in 2007 to this end.
Florian Sikora started a PhD on algorithmic aspects of biological
networks under the supervision of Guillaume Blin and Stéphane Vialette
The aim of this project is thus two-fold:
to strengthen the AlgoB team to make it
an attractive place for young dynamic researchers
(this includes conducting our ambitious project in close
partnership with our well-established national and international
and carefully expanding our collaborations with labs of intersecting
interests and complementary strengths.
The present project is composed of 3 parts (tasks):
(i) future research directions and open problems that stem
from our work,
(ii) new research directions.
Part~1 presents our perspectives on $d$-intervals and
$d$-interval related graphs, and linear graphs,
pattern matching for permutations and contact maps
(starting collaboration with Minghui Jiang, Utah University, USA).
Part~2 is concerned with biological networks. We present in this
section our theoretical and practical perspectives on biological
(collaboration with University of Milano-Bicocca, Italy,
University of Bergamo, Italy, University of Barcelona Spain).
Finally, Part~3 is devoted to presenting a new project on radiotherapy
settings (starting collaboration with Warsaw University, Poland).
Monsieur Guillaume BLIN (UNIVERSITE PARIS-EST MARNE LA VALLEE) – firstname.lastname@example.org
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
UPEMLV UNIVERSITE PARIS-EST MARNE LA VALLEE
Help of the ANR 161,790 euros
Beginning and duration of the scientific project: - 48 Months