@comment{{Stuart Pook, $Id: publications.bib,v 1.54 2005/04/28 14:00:04 stuart Exp $ }}
  author = {Stuart Pook},
  title = {Interaction and Context in Zoomable User Interfaces},
  school = {École Nationale Supérieure des Télécommunications},
  address = {France},
  month = jun,
  year = 2001,
  url = { },
  abstract = {

Many interactive computer systems use menus as an important part of their interface.
Menus allow users to select operations but not to control their execution.
A second interactor, such as a dialog box, has to be used
to control the chosen operation and thus complete the interaction.
This decomposition of what is a single action from the user's point of view into two
distinct steps slows down interaction with computer systems.
This thesis proposes a new contextual pop-up menu,
called a Control Menu,
that includes proportional control of the chosen operation with immediate feedback.
Using this menu gives a more fluid control of complex interfaces and
has the advantage of an expert form of use that is very similar to,
and thus easily learnt from, the novice usage.

Interaction with databases and navigation within large information spaces are
important tasks in many applications.
Many visualization systems cause user disorientation
as users find it difficult to understand their position within the information space and
to locate desired information.
This thesis proposes several new contextual aids for Zoomable User Interfaces
that address these issues.

The first aid, a hierarchical view of the information space,
helps users understand their current position and the location of the desired information,
and accelerates navigation.
The second type of aid uses dynamically generated transparent and temporary views that are
created and controlled by users in a single gesture.
These interactive views overlay the current view of the focus with contextual or historical
information which shows users what surrounds the current view or the route
taken to arrive at that view.
The effective use of these new aids requires a tight coupling between
interaction and presentation which
is achieved via the use of Control Menus.
  author = {Stuart L. Pook},
  title = {Synthetic Portfolios and Currency Options},
  school = {Department of Econometrics, The University of Sydney},
  address = {Australia},
  type = {{B.Ec} {H}onour's thesis},
  year = 1986,
  pdf = {operations-research-thesis.pdf}
  author = {Stuart Leonard Pook},
  title = {Experiments with machine-readable dictionaries},
  school = {Basser Department of Computer Science, The University of Sydney},
  address = {Australia},
  type = {{B.Ec} {H}onour's thesis},
  year = 1987,
  month = dec,
  pdf = {computer-science-thesis.pdf},
  abstract = {
		Machine-readable dictionaries are just starting to become available
		to information scientists and lexicographers.  Many other databases
		of machine-readable text such as news wires, library catalogues
		and collections of scientific papers are also becoming available
		as well as increasing in size and coverage.  New sets of tools
		are required to efficiently store and access these new sources of
		information.  This thesis explores some of the ways that machine-
		readable dictionaries and thesauri can be used in the transmission
		and retrieval of these new databases.
		A piece of text must first be understood before it can be
		processed by an intelligent retrieval system.  The most basic
		level of understanding is at the word level; the computer needs
		to understand in which sense the words in the text are being used.
		Machine-readable dictionaries and thesauri can be used in this task
		provided they are first stored in suitable databases.  Once the
		pieces of text have been analysed they must then be classified and
		transmitted.  Then the user of a database must be provided with the
		tools necessary to retrieve interesting items.  Algorithms that
		can be used to implement new methods of text retrieval and the
		ways in which they can be used in commercial products are presented.
  title = {Making sense out of searching},
  author = {Stuart L. Pook and Jason Catlett},
  booktitle = {Proceedings of the Online Information Conference},
  year = 1988,
  pages = { 69-78 },
  month = jan,
  address = {Sydney, NSW, Australia},
  organization = {Library Association of Australia (Information Science Section)},
  isbn = {0 86804 089 4},
  pdf = {online.pdf},
  abstract = {
		The trouble with text retrieval using keywords is that
		English words are imprecise: there may be many words for
		the entity the user wants, and each of these may also
		have other (unintended) meanings.  To get closer to the
		dream of `retrieve what I mean, not what I say,' systems
		need to take into account the sense in which each word is
		used in the text stored, and to get from the user a more
		precise and complete statement of the concept sought.
		Recent research on machine-readable dictionaries and
		thesauri may soon make this a reality.
	title=Integrated construction of a human chromosome 21 YAC contig map,
	author=Ilia Chumakov and Roland Heilig and Philippe Rigault and
		Le Gall, Isabell and Gerard Frelat and Pascal Soularue and
		Emmanuel Barillot and Christine Bellann\'e-Chantelot
		and Stuart Pook and Guy Vaysseix and Jean Weissenbach
		and Pierre Ougen and Alain Billaut and Le Paslier, Denis
		and Daniel Cohen,
	booktitle=Abstracts of papers presented at the 1992 meeting on Genome Mapping and Sequencing,
	year = 1992,
	month = may,
	address = Cold Spring Harbor, NY, USA,
	organization = Cold Spring Harbor Laboratory,
	pages =  131 
	title=Accelerated physical mapping of the human genome,
	author=Daniel Cohen and Christine Bellann\'e-Chantelot and
		Emmanuel Barillot and Bruno Lacroix and Isabelle Gros
		and Sandrine Beaufils and Fabrice Glibert and Laurent
		Susini and Isabelle Georges and Guy Vaysseix and Philippe
		Gesnouin and Stephane Bertrand and Georges Lucotte and
		Jacqueline M\'eny and Stuart Pook and Alain Billaut and
		Pierre Ougen and Hadi Abderrahim and Le Paslier, Denis,
	booktitle=Abstracts of papers presented at the 1992 meeting on Genome Mapping and Sequencing,
	year = 1992,
	month = may,
	address = Cold Spring Harbor, NY, USA,
	organization = Cold Spring Harbor Laboratory,
	pages =  32 ,
  author = {Christine Bellann{\'e}-Chantelot and Bruno Lacroix and
		Pierre Ougen and Alain Billaut and Sandrine Beaufils and
		St{\'e}phane Bertrand and Isabelle Georges and
		Fabrice Glibert and Isabelle Gros and
		Georges Lucotte and Laurent Susini and
		Jean-Jacques Codani and Philippe Gesnouin and
		Stuart Pook and Guy Vaysseix and Jennifer Lu-Kuo and
		Thomas Ried and David Ward and Ilya Chumakov and
		Le Paslier, Denis and Emmanuel Barillot and
		Daniel Cohen},
  title = {Mapping the Whole Human Genome
		by Fingerprinting Yeast Artificial Chromosomes},
  journal = {Cell},
  year = 1992,
  month = sep,
  volume = 70,
  pages = {1059-1068},
  abstract = { Physical mapping of the human genome has until now
		been envisioned through single chromosome strategies.
		We demonstrate that by using the large insert yeast
		artificial chromosomes (YACs) a whole genome approach
		becomes feasible. YACs (22,000) of 810 kb
		mean size (5 genome equivalents) have been fingerprinted
		to obtain individual patterns of restriction fragments
		detected by a LINE-1 (L1) probe. More than 1000
		contigs were assembled. Ten randomly chosen contigs
		were validated by metaphase chromosome fluorescence
		in situ hybridization, as well as by analyzing
		the inter-Alu PCR patterns of their constituent YACs.
		We estimate that 15% to 20% of the human genome,
		mainly the L1-rich regions, is already covered with
		contigs larger than 3 Mb.
  url = { }
  title = {Continuum of overlapping clones spanning the entire human chromosome 21q},
  author = { Ilya Chumakov and Phillipe Rigault and Sophie Guillou
		and Pierre Ougen and Alain Billault and Ghislaine Guasconi
		and Patricia Gervy and Isabelle LeGall and Pascal Soularue
		and Laurent Grinas and Lydie Bougueleret and Christine
		Bellann{\'e}-Chantelot and Brune Lacroix and Emmanuel
		Barillot and Philippe Gesnouin and Stuart Pook and
		Guy Vaysseix and Gerard Frelat and Annette Schmitz and
		Jean-Luc Sambucy and Assumpcio Bosch and Xavier Estivill
		and Jean Weissenbach and Alain Vignal and Harold Riethman
		and David Cox and David Patterson and Kathleen Gardiner
		and Masahira Hattori and Yoshiyuki Sakaki and Hitoshi
		Ichikawa and Misao Ohki and Le Paslier, Denis and Roland
		Heilig and Stylianos Antonarakis and Daniel Cohen},
  journal = {Nature},
  pages = {380-387},
  year = 1992,
  month = oct,
  volume = 359,
  abstract = { A continuous array of overlapping clones covering
		the entire human chromosome 21q was contructed
		from human yeast artificial chromosome libraries using
		sequence-tagged sites as landmarks specifically detected
		by polymerase chain reaction. The yeast artificial
		chromosome contiguous unit starts with pericentromeric
		and ends with subtelomeric loci of 21q. The resulting
		order of sequence-tagged sites is consistent with other
		physical and genetic mapping data. This set of overlapping
		clones will promote our knowledge of the structure of
		this chromosome and the function of its genes.
  url = { }
	title = Environment for G\'en\'ethon large scale physical mapping,
	author = Bruno Lacroix and Jean-Jacques Codani and Philippe
		Gesnouin and Eric Viara and Stuart Pook and Guy Vaysseix
		and Daniel Cohen and Emmanuel Barillot,
	pages =106,
	booktitle=Abstracts of papers presented at the 1993 meeting on Genome Mapping and Sequencing,
	year = 1993,
	month = may,
	address = Cold Spring Harbor, NY, USA,
	organization = Cold Spring Harbor Laboratory,
  title = {The {IDB} database system and its use in the human genome project: {HUGEMAP}},
  author = {Eric Viara and Stuart Pook and Bruno Lacroix and
		Michel Tissot and Laurent Atlan and Annick Cohen-Akenine and
		Guy Vaysseix and Emmanuel Barillot},
  booktitle = {Interconnection of Molecular Biology Databases},
  year = 1994,
  month = aug,
  address = {Stanford, CA, USA},
  organization = {SRI International Artificial Intelligence Center},
  note = { only published electronically},
  html = {mimbd94.html}
	title = New concepts for navigation and visualisation in biological databases,
	author = Frédéric Guyon and Stuart Pook and Guy Vaysseix and Emmanuel Barillot,
	booktitle=Human Genome Meeting: Meeting Programme and Abstract Book,
	year = 1998,
	month = mar,
	address = Turin, Italy,
	organization = The Human Genome Organisation, One Park Square West, London NW1 4LJ, United Kingdom,
	pages = 27,
	html = hgm98.html,
  booktitle = {Objects in Bioinformatics '98},
  year = 1998,
  month = aug,
  address = {Hinxton Hall, Cambridge, UK},
  organization = {European Bioinformatics Institute},
  title = {Distributing and Visualising Biological Objects at Infobiogen},
  author = {Eric Viara and Stuart Pook and Fr{\'e}d{\'e}ric Guyon and
		Christophe Cussat-Blanc and Guy Vaysseix and Emmanuel Barillot},
  html = {viara.html},
  abstract = {
		Our aim is to design a complete object-oriented environment for biological
		data management. In that respect, Sysra Informatique and Infobiogen first
		developed an object-oriented database management system EyeDB with funding
		from Sysra Informatique, ANVAR and the EC BIOTECH program. Then we have
		implemented a complete Java mapping of the EyeDB object model.
		We also designed a CORBA layer on top of EyeDB. An ad-hoc compiler can
		automatically generate an IDL and an ORB server from the database schema. A
		language allows to define a more elaborate mapping from the database schema to
		a target IDL. This allows to export different views from the same database. It
		also permits to target a common IDL from databases with different schemas.
		We believe that the biological community should now adopt a standard to define
		the semantic of its objects.  With colleagues at EBI (Patricia Rodriguez-Tomé
		et al), we have defined a standard description for the genome maps in the
		form of an IDL and we submit it to the bioinformatic community for adoption
		and comments. This is done through the Life Sciences Research Task Force of
		the Object Management Group.
		Biological data now constitutes a huge amount of information with which it is
		difficult to interact. Particularly it is quite impossible to visualise these
		large spaces of information with the traditional display techniques. We propose
		to use new concepts of visualisation and navigation well suited for huge
		volume of data. We have implemented these new concepts in two applications:
		a map viewer, (MappetShow) that gives a clear view of very dense
		maps (several hundreds of markers); it uses the following concepts:
		(multi-)focus+context techniques, dynamic layout, multi-scaling
		a generic navigator for large information spaces: Zomit. It consists
		of a generic Java applet client and a C++ library used to develop a
		server. It has been used to implement a genome browser: ZoomMap. It
		is based on the concepts of zooming, semantic zooming, portals and
		magic lenses.
  author = {Stuart Pook and Guy Vaysseix and Emmanuel Barillot},
  title = {Zomit: biological data visualization and browsing},
  year = 1998,
  pages = {807-814},
  issn = { 1367-4803 },
  month = oct,
  volume = 14,
  number = 9,
  journal = {Bioinformatics},
  abstract = {
		Motivation: The problems caused by the difficulty in visualizing and
		browsing biological databases have become crucial. Scientists can
		no longer interact directly with the huge amount of available data.
		However future breakthroughs in biology depend on this interaction.
		We propose a new metaphor for biological data visualization and browsing
		that allows navigation in very large databases in an intuitive way.
		The concepts underlying our approach are based on navigation and
		visualization with zooming, semantic zooming, and portals; and on data
		transformation via magic lenses. We think that these new visualization
		and navigation techniques should be applied globally to a federation
		of biological databases. Results: We have implemented a generic tool,
		called Zomit, that provides an application programming interface
		for developing servers for such navigation and visualization, and a
		generic architecture-independent client (Java applet) that queries
		such servers. As an illustration of the capabilities of our approach,
		we have developed ZoomMap, a prototype browser for the Hugemap human
		genome map database. Availability: Zomit and ZoomMap are available at
		the URL
  url = { },
  pdf = {bioinformatics1998.pdf}
  title = {The {HuGeMap} Database: interconnection and
			visualization of human genome maps},
  author = {Emmanuel Barillot and Stuart Pook and
			Fr{\'e}d{\'e}ric Guyon and Christophe Cussat-Blanc and
			{\'E}ric Viara and Guy Vaysseix},
  journal = {Nucleic Acids Research},
  volume = 27,
  number = 1,
  pages = {119-122},
  year = 1999,
  url = {},
  pdf = {NAR1999.pdf},
  abstract = {The HuGeMap database stores the major genetic and
		physical maps of the human genome. HuGeMap is accessible
		on the Web at
		and through a CORBA server. A standard genome
		map data format for the interconnection of genome
		map databases was defined in collaboration with
		the EBI. The HuGeMap CORBA server provides this
		interconnection using the interface definition language
		IDL. Two graphical user interfaces were developed
		for the visualization of the HuGeMap data: ZoomMap
		) for navigation by zooming and data
		transformation via magic lenses, and MappetShow
		( ) for
		visualizing and comparing maps. }
  author = {Stuart Pook and Eric Lecolinet and Guy Vaysseix and Emmanuel Barillot},
  title = {Control Menus: Execution and Control in a Single Interactor},
  booktitle = {CHI 2000 Extended Abstracts},
  pages = {263-264},
  key = {CHI},
  address = {The Hague, The Netherlands},
  year = 2000,
  month = apr,
  organization = {ACM Press},
  abstract = {
		We propose a new type of contextual pop-up menu called
		a control menu.  These menus combine the selection
		of an operation and the control of this operation.
		They integrate up to two scroll bars or spin-boxes and
		thus allow users to keep their attention focused on
		the menu during the operation. Control menus can have
		sub-menus, and also retain the novice and expert modes
		of use found in marking menus.
		We describe control menus and how they are useful
		in different types of user interfaces.	A program
		incorporating our control menus can be tested at
  url = { },
  pdf = {chi2000.pdf},
  isbn = {1-58113-216-6}
  author = {Stuart Pook and Eric Lecolinet and Guy Vaysseix and Emmanuel Barillot},
  title = {Context and Interaction in Zoomable User Interfaces},
  booktitle = {AVI 2000},
  key = {AVI},
  address = {Palermo, Italy},
  year = 2000,
  month = may,
  organization = {ACM Press},
  abstract = {
		Zoomable User Interfaces (ZUIs) are difficult to use on
		large information spaces in part because they provide
		insufficient context.  Even after a short period of
		navigation users no longer know where they are in the
		information space nor where to find the information they
		are looking for.  We propose a temporary in-place context
		aid that helps users position themselves in ZUIs.  This
		context layer is a transparent view of the context that
		is drawn over the users' focus of attention.  A second
		temporary in-place aid is proposed that can be used to
		view already visited regions of the information space.
		This history layeris an overlapping transparent layer
		that adds a history mechanism to ZUIs.	We complete
		these orientation aids with an additional window, a
		hierarchy tree, that shows users the structure of the
		information space and their current position within it.
		Context layers show users their position, history layers
		show them how they got there, and hierarchy trees show
		what information is available and where it is.

		ZUIs, especially those that include these new orientation
		aids, are difficult to use with standard interaction
		techniques.  They provide a large number of commands
		which must be used frequently and on a changing image.
		The mouse and its buttons cannot provide a rapid access to
		all these commands without new interaction techniques.
		We propose a new type of menu, a control menu that
		facilitates the use of ZUIs and which we feel can also
		be useful in other types of applications.
  pages = {227-231 \& 317},
  url = { },
  pdf = {avi2000.pdf}
  author = {Stuart Pook and Eric Lecolinet and Guy Vaysseix and Emmanuel Barillot},
  title = {Contexte et Interaction dans les Interfaces Zoomables},
  booktitle = {RJC-IHM 2000},
  key = {RJCIHM},
  address = {L'Île de Berder, France},
  year = 2000,
  month = may,
  organization = {Laboratoire VALORIA (Université de Bretagne-Sud)},
  abstract = {
		Les interfaces zoomables (IZs) sont difficiles à
		utiliser sur un grand espace d'information, en partie
		parce qu'elles ne fournissent pas suffisamment de
		contexte à l'utilisateur. Même après une courte période
		d'utilisation, les utilisateurs ne savent plus où ils
		sont dans l'espace d'information ni ce qu'ils sont
		en train de regarder. Nous proposons deux nouvelles
		aides temporaires, une couche de contexte et une couche
		historique, qui aident les utilisateurs à se situer dans
		l'espace d'information. Elles sont transparentes et
		sont dessinées sur le focus de telle sorte que l'aide et
		le focus sont visibles. La couche de contexte contient
		une vue du contexte et aide l'utilisateur à se situer
		dans l'espace d'information. Avec la couche historique
		l'utilisateur peut revisiter le chemin parcouru dans
		l'espace d'information. Nous complétons ces aides avec
		une fenêtre supplémentaire qui montre à tout moment la
		structure de l'espace d'information et la position de
		l'utilisateur dans cet espace.

		De plus, il est difficile d'interagir avec des IZs avec
		des modèles classiques d'interaction. Les IZs fournissent
		des commandes qui doivent être utilisées souvent sur une
		image très changeante.	La souris et ses boutons sont trop
		limités pour un accès rapide à toutes ces commandes sans
		l'utilisation de nouvelles techniques d'interaction.
		Nous présentons un nouveau type de menu, un control
		menu, qui facilite l'accès rapide à ces commandes.
		Notre IZ inclut ces nouvelles techniques et peut être
		testée à l'URL
  url = { },
  pdf = {rjcihm2000.pdf},
  pages = {57-60}
  author = { Eric Lecolinet and Claudie Faure and Isabelle Demeure amd
		Jean-Claude Moissinac and Stuart Pook },
  title = { Augmentation de cours et de réunion dans un Campus },
  booktitle = { 2nd French-speaking conference on Mobility and uibquity computing },
  address = { Grenoble, France },
  pages = { 161-168 },
  organization = { ACM Press },
  month = may,
  year = 2005,
  isbn = { 1-59593-172-4 }
  author = {Isabelle Demeure and Claudie Faure and
		Eric Lecolinet and Jean-Claude Moissinac and Stuart Pook},
  title = {Mobile Computing to Facilitate Interaction in
		Lectures and Meetings},
  booktitle = {DFMA 2005},
  key = {DFMA-2005},
  address = {Besançon, France},
  year = 2005,
  month = feb,
  pages = {359-366},
  pdf = {DFMA05.pdf},
  organization = {IEEE Computer Society},
  abstract = {The Campus Mobile project explored how PDAs and
	innovative interfaces can improve interaction during lectures and
	in small meetings. These mobile computers (small pcs or pdas)
	are nomad mediators that provide the link between the public
	space and the users private space. A lecturer uses an augmented
	whiteboard to annotate her presentation, while the slides and
	annotations are broadcast in real time to the students pdas. The
	students can also annotate the presentation. They can then replay
	the lecture at their leisure. We developed and tested the user
	interfaces for the interactions on the whiteboard and on the
	pdas, the data formats to store the annotations and temporal
	data, and the network protocol for reliable wireless broadcast
	transmission. Small meetings have a very different interaction
	pattern. Instead of a lecturer that transmits knowledge, the
	participants collaborate in modifying documents. We developed
	groupware services that encourage these interactions and show
	how the different interaction patterns imply different network
  author = {Stuart Pook and Eric Lecolinet and Guy Vaysseix and Emmanuel Barillot},
  title = {Des aides transparentes de navigation et
			un nouveau type de menu
			pour les interfaces zoomables},
  booktitle = {ERGO-IHM 2000},
  key = {ERGO-IHM2000},
  address = {Biarritz, France},
  year = 2000,
  month = oct,
  url = { },
  pdf = {ihm2000.pdf},
  organization = {CRT ILS \& ESTIA},
  pages = {170-177},
  isbn = {2-9514772-0-1},
  abstract = {
		Le fait que les interfaces zoomables (IZs) fournissent généralement peu
		de contexte peut parfois rendre leur utilisation difficile.
		Les utilisateurs ont rapidement tendance à ne plus savoir
		où ils sont dans l'espace d'information ni ce qu'ils sont en train de regarder.
		Nous proposons deux aides temporaires et transparentes qui montrent à l'utilisateur sa position
		dans l'espace d'information.
		Nous proposons également une représentation hiérarchique qui indique en permanence
		la structure de l'espace d'information et la position de l'utilisateur dans cette structure.
		Les IZs soulèvent également un problème d'interaction.
		Leurs commandes sont fréquemment utilisées et sur une interface
		changeante :
		le modèle WIMP est alors trop limité pour un accès rapide à toutes ces commandes
		sans l'utilisation de nouvelles techniques d'interaction.
		Nous présentons un nouveau type de
		menu, nommé control menu, qui facilite l'accès rapide à ces commandes
		et qui peut être utile dans d'autres types d'applications.
  author = { Patricia Plénacoste and Eric Lecolinet and Stuart Pook and
		Cédric Dumas and Jean-Daniel Fekete },
  title = { Zoomable and 3D Representations for Digital Libraries },
  booktitle = { IHM-HCI 2001 },
  address = { Lille, France },
  month = sep,
  year = 2001
  author = { Eric Lecolinet and Jean-Daniel Fekete and Stuart Pook},
  title = { Bibliothèques~: comparaisons entre le réel et le virtuel en
		{3D}, {2D} zoomable et {2D} arborescent },
  booktitle = { ASTI 2001 },
  key = { ASTI },
  year = 2001,
  month = apr,
  pages = { 24-25 },
  html = {asti2001/index.html},
  organization = {Association Française des Sciences et Technologies de l'Information},
  address = { Cité des Sciences et de l'Industrie, Paris }
  title = {Control menus et vues contextuelles pour les interfaces zoomables},
  author = { Stuart Pook and Eric Lecolinet and Guy Vaysseix and Emmanuel Barillot },
  journal = { Revue d'Interaction Homme-Machine },
  year = 2003,
  volume = 4,
  number = 1,
  pages = { 59-84 },
  publisher = { Europia Productions },
  address = { Paris, France },
  issn = {1289-2963 },
  pdf = {rihm2003.pdf},
  abstract = {
		Les interfaces zoomables constituent un outil intéressant pour visualiser
		des espaces infor mationnels de grande taille. Cependant, le fait que
		ces interfaces fournissent généralement peu de contexte peut parfois
		rendre leur utilisation délicate. Les utilisateurs ont tendance à
		avoir du mal à se localiser précisément dans l'espace d'infor mation
		et à déter miner avec certitude la nature de leur point de focus. Nous
		proposons deux nouvelles aides temporaires transparentes qui facilitent
		la contextualisation du focus courant dans l'espace d'infor mation. Nous
		proposons également une représentation hiérarchique qui indique en
		per manence la structure de l'espace d'infor mation et la position
		de l'utilisateur dans cette structure. Nous proposons par ailleurs
		un nouveau type de menu contextuel, appelé « Control menu », qui
		permet de fluidifier l'interaction en sélectionnant et en contrôlant
		les opérations en un seul geste. Bien que son utilisation ne soit
		pas limitée à ce type d'interfaces, ce nouveau type de menu semble
		particulièrement bien adapté aux interfaces qui nécessitent de fréquentes
		interactions comme les interfaces zoomables. Deux interfaces zoomables
		implémentant ces nouvelles techniques peuvent être testées à l'URL
  title = {Interfaces zoomables et Control menus. Techniques focus+contexte pour la navigation interactive dans les bases de données},
  author = { Eric Lecolinet and Stuart Pook },
  journal = { Les cahiers du numérique },
  year = 2002,
  month = dec,
  publisher = { Lavoisier },
  address = { Paris, France },
  pages = { 191-210 },
  isbn = {2-7462-0578-5},
  volume = 3,
  number = {3/2002},
  pdf = {cahiers-num02.pdf}
  title = {NaviCell: a web-based environment for
		navigation, curation and maintenance of large
		molecular interaction maps},
  author = {Inna Kuperstein and David PA Cohen and Stuart Pook and
		Eric Viara and Laurence Calzone and Emmanuel Barillot and Andrei Zinovyev},
  journal = {BMC Systems Biology},
  year = 2013,
  month = oct,
  volume = {7},
  number = {100},
  abstract = {
Background: Molecular biology knowledge can be formalized and
systematically represented in a computer- readable form as a comprehensive
map of molecular interactions. There exist an increasing number of maps
of molecular interactions containing detailed and step-wise description
of various cell mechanisms. It is difficult to explore these large maps,
to organize discussion of their content and to maintain them. Several
efforts were recently made to combine these capabilities together in
one environment, and NaviCell is one of them.

Results: NaviCell is a web-based environment for exploiting large maps
of molecular interactions, created in CellDesigner, allowing their
easy exploration, curation and maintenance. It is characterized by
a combination of three essential features: (1) efficient map browsing
based on Google Maps; (2) semantic zooming for viewing different levels of
details or of abstraction of the map and (3) integrated web-based blog for
collecting community feedback. NaviCell can be easily used by experts in
the field of molecular biology for studying molecular entities of interest
in the context of signaling pathways and crosstalk between pathways within
a global signaling network.  NaviCell allows both exploration of detailed
molecular mechanisms represented on the map and a more abstract view
of the map up to a top-level modular representation. NaviCell greatly
facilitates curation, maintenance and updating the comprehensive maps
of molecular interactions in an interactive and user-friendly fashion
due to an imbedded blogging system.

Conclusions: NaviCell provides user-friendly exploration of large-scale
maps of molecular interactions, thanks to Google Maps and WordPress
interfaces, with which many users are already familiar. Semantic zooming
which is used for navigating geographical maps is adopted for molecular
maps in NaviCell, making any level of visualization readable. In addition,
NaviCell provides a framework for community-based curation of maps.

Keywords: Biological network, Comprehensive map of molecular interactions,
Google maps, Semantic zooming, Modules in biological networks, Blogging
interaction maps
  publisher = { BioMed Central },
  url = {}
  title = { Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial },
  author = { Nicolas Servant and Julien Roméjon and Pierre Gestraud and Philippe La Rosa and Georges Lucotte and Séverine Lair and Virginie Bernard and Bruno Zeitouni and Fanny Coffin and Gérôme Jules-Clément and Florent Yvon and Alban Lermine and Patrick Poullet and Stéphane Liva and Stuart Pook and Tatiana Popova and Camille Barette and François Prud’homme and Jean-Gabriel Dick and Maud Kamal and Christophe Le Tourneau and Emmanuel Barillot and and Philippe Hupé },
  journal = {Frontiers in Genetics},
  year = 2014,
  month = may,
  volume = {5},
  number = {152},
  pdf = {2014_Servant_SHIVA.pdf},
  abstract = {
Precision medicine (PM) requires the delivery of individually
adapted medical care based on the genetic characteristics of
each patient and his/her tumor. The last decade witnessed the
development of high-throughput technologies such as microarrays and
next-generation sequencing which paved the way to PM in the field
of oncology. While the cost of these technologies decreases, we are
facing an exponential increase in the amount of data produced. Our
ability to use this information in daily practice relies strongly on the
availability of an efficient bioinformatics system that assists in the
translation of knowledge from the bench towards molecular targeting and
diagnosis. Clinical trials and routine diagnoses constitute different
approaches, both requiring a strong bioinformatics environment capable
of (i) warranting the integration and the traceability of data, (ii)
ensuring the correct processing and analyses of genomic data, and
(iii) applying well-defined and reproducible procedures for workflow
management and decision-making. To address the issues, a seamless
information system was developed at Institut Curie which facilitates the
data integration and tracks in real-time the processing of individual
samples. Moreover, computational pipelines were developed to identify
reliably genomic alterations and mutations from the molecular profiles
of each patient. After a rigorous quality control, a meaningful report
is delivered to the clinicians and biologists for the therapeutic
decision. The complete bioinformatics environment and the key points of
its implementation are presented in the context of the SHIVA clinical
trial, a multicentric randomized phase II trial comparing targeted
therapy based on tumor molecular profiling versus conventional therapy in
patients with refractory cancer. The numerous challenges faced in practice
during the setting up and the conduct of this trial are discussed as an
illustration of PM application.

Keywords: precision medicine, clinical trial, bioinformatics, sequencing, oncology, SHIVA
  url = { }

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