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Advancing cancer systems biology: introducing the Center for the Development of a Virtual Tumor, CViT.

Deisboeck TS, Zhang L, Martin S - Cancer Inform (2007)

Bottom Line: Integrative cancer biology research relies on a variety of data-driven computational modeling and simulation methods and techniques geared towards gaining new insights into the complexity of biological processes that are of critical importance for cancer research.These include the dynamics of gene-protein interaction networks, the percolation of sub-cellular perturbations across scales and the impact they may have on tumorigenesis in both experiments and clinics.Such innovative 'systems' research will greatly benefit from enabling Information Technology that is currently under development, including an online collaborative environment, a Semantic Web based computing platform that hosts data and model repositories as well as high-performance computing access.

View Article: PubMed Central - PubMed

Affiliation: Complex Biosystems Modeling Laboratory, Harvard-MIT (HST) Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA. deisboec@helix.mgh.harvard.edu

ABSTRACT
Integrative cancer biology research relies on a variety of data-driven computational modeling and simulation methods and techniques geared towards gaining new insights into the complexity of biological processes that are of critical importance for cancer research. These include the dynamics of gene-protein interaction networks, the percolation of sub-cellular perturbations across scales and the impact they may have on tumorigenesis in both experiments and clinics. Such innovative 'systems' research will greatly benefit from enabling Information Technology that is currently under development, including an online collaborative environment, a Semantic Web based computing platform that hosts data and model repositories as well as high-performance computing access. Here, we present one of the National Cancer Institute's recently established Integrative Cancer Biology Programs, i.e. the Center for the Development of a Virtual Tumor, CViT, which is charged with building a cancer modeling community, developing the aforementioned enabling technologies and fostering multi-scale cancer modeling and simulation.

No MeSH data available.


Related in: MedlinePlus

CViT Annotation System.
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Related In: Results  -  Collection

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f4-cin-05-01: CViT Annotation System.

Mentions: Cancer research has always been an international enterprise with pockets of critical expertise being developed at numerous sites all over the world and thus now, more so than ever, large-scale consortium projects have to go beyond institutional boundaries to accomplish a set task that would otherwise exceed the resources available at a single site. Given the fact that this entails setup and management of long-distance collaborations that also cross multiple disciplines, a new more flexible collaborative environment has to be created. CViT has built such a user-friendly online platform, CViT. org (URL: http://www.cvit.org) that employs a username & password-protected ‘wiki’-type environment to post and discuss content (Figure 2, left). A relatively large portion of the regularly updated information such as researcher profiles (Figure 2, right), resources, tutorials and software tools, is already publicly-accessible as part of CViT’s commitment to community outreach. For the continuously growing CViT group of investigators which includes scientists from dozens of institutions around the world, CViT.org provides its participating investigators a number of advanced tools to rapidly communicate, thus facilitating dissemination of knowledge and fostering collaborations: (1) CViT.org offers “digital notebooks” or blogs such as “Ask the Expert” that have investigators present (on the basis of their PubMedlinked abstracts) one of their recent publications to the group, thereby soliciting feedback and thus setting up a lively discussion forum (Figure 3, left). Another blog, “CViT Recommends” is focused on suggestions and recommendations of useful information, including links to up-to-date reviews and upcoming meetings relevant to the field. (2) Secondly, really simple syndication (RSS) is a document specification that gives users the power to collect and organize Web-based news and information in a more efficient manner. CViT RSS feeds are intended to encourage CViT members to participate in ongoing discussions within CViT and to facilitate access to and dissemination of cancer modeling-focused, public information. Currently, the site provides news feeds on activity within its own blogs (Figure 3, right), on cancer research and, more generally, science news as well as on peer-reviewed literature relevant to cancer modeling efforts. (3) Thirdly, CViT.org broadcasts news, announcements and notifications using its mail list server to its membership as well as to the computational biology groups of the entire ICBP. (4) Lastly, an annotation system (Figure 4) provided by IBM makes it convenient for CViT’s members to annotate research documents in a variety of formats such as MS Word, PDF and others. This enables capture, collection, management, access and exchange of any such annotations across the distributed teams.


Advancing cancer systems biology: introducing the Center for the Development of a Virtual Tumor, CViT.

Deisboeck TS, Zhang L, Martin S - Cancer Inform (2007)

CViT Annotation System.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2666954&req=5

f4-cin-05-01: CViT Annotation System.
Mentions: Cancer research has always been an international enterprise with pockets of critical expertise being developed at numerous sites all over the world and thus now, more so than ever, large-scale consortium projects have to go beyond institutional boundaries to accomplish a set task that would otherwise exceed the resources available at a single site. Given the fact that this entails setup and management of long-distance collaborations that also cross multiple disciplines, a new more flexible collaborative environment has to be created. CViT has built such a user-friendly online platform, CViT. org (URL: http://www.cvit.org) that employs a username & password-protected ‘wiki’-type environment to post and discuss content (Figure 2, left). A relatively large portion of the regularly updated information such as researcher profiles (Figure 2, right), resources, tutorials and software tools, is already publicly-accessible as part of CViT’s commitment to community outreach. For the continuously growing CViT group of investigators which includes scientists from dozens of institutions around the world, CViT.org provides its participating investigators a number of advanced tools to rapidly communicate, thus facilitating dissemination of knowledge and fostering collaborations: (1) CViT.org offers “digital notebooks” or blogs such as “Ask the Expert” that have investigators present (on the basis of their PubMedlinked abstracts) one of their recent publications to the group, thereby soliciting feedback and thus setting up a lively discussion forum (Figure 3, left). Another blog, “CViT Recommends” is focused on suggestions and recommendations of useful information, including links to up-to-date reviews and upcoming meetings relevant to the field. (2) Secondly, really simple syndication (RSS) is a document specification that gives users the power to collect and organize Web-based news and information in a more efficient manner. CViT RSS feeds are intended to encourage CViT members to participate in ongoing discussions within CViT and to facilitate access to and dissemination of cancer modeling-focused, public information. Currently, the site provides news feeds on activity within its own blogs (Figure 3, right), on cancer research and, more generally, science news as well as on peer-reviewed literature relevant to cancer modeling efforts. (3) Thirdly, CViT.org broadcasts news, announcements and notifications using its mail list server to its membership as well as to the computational biology groups of the entire ICBP. (4) Lastly, an annotation system (Figure 4) provided by IBM makes it convenient for CViT’s members to annotate research documents in a variety of formats such as MS Word, PDF and others. This enables capture, collection, management, access and exchange of any such annotations across the distributed teams.

Bottom Line: Integrative cancer biology research relies on a variety of data-driven computational modeling and simulation methods and techniques geared towards gaining new insights into the complexity of biological processes that are of critical importance for cancer research.These include the dynamics of gene-protein interaction networks, the percolation of sub-cellular perturbations across scales and the impact they may have on tumorigenesis in both experiments and clinics.Such innovative 'systems' research will greatly benefit from enabling Information Technology that is currently under development, including an online collaborative environment, a Semantic Web based computing platform that hosts data and model repositories as well as high-performance computing access.

View Article: PubMed Central - PubMed

Affiliation: Complex Biosystems Modeling Laboratory, Harvard-MIT (HST) Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA 02129, USA. deisboec@helix.mgh.harvard.edu

ABSTRACT
Integrative cancer biology research relies on a variety of data-driven computational modeling and simulation methods and techniques geared towards gaining new insights into the complexity of biological processes that are of critical importance for cancer research. These include the dynamics of gene-protein interaction networks, the percolation of sub-cellular perturbations across scales and the impact they may have on tumorigenesis in both experiments and clinics. Such innovative 'systems' research will greatly benefit from enabling Information Technology that is currently under development, including an online collaborative environment, a Semantic Web based computing platform that hosts data and model repositories as well as high-performance computing access. Here, we present one of the National Cancer Institute's recently established Integrative Cancer Biology Programs, i.e. the Center for the Development of a Virtual Tumor, CViT, which is charged with building a cancer modeling community, developing the aforementioned enabling technologies and fostering multi-scale cancer modeling and simulation.

No MeSH data available.


Related in: MedlinePlus