Help Resources/Cellucidate Content
Catalogue of public cBooks: General Biology
Cellucidate Support Dec 08, 2009
This list includes publicly available cBooks on Cellucidate with rich content that will be of interest to other Cellucidate users, either for the purposes of demonstrating how Cellucidate can be used or as sets of agents and rules that could serve as a foundation for new models or be incorporated into existing models. This list is by no means complete and will updated periodically.
Do you have a cBook that you are willing to make publicly available and that you think might be of interest to others?
Just respond to this discussion topic with a link to your cBook and a brief description of why you think it might be of interest to other users and we might incorporate it into a future edition of the catalog :-)
So without further ado, the nominations in the category General Biology are ...
Biorhythms Newsletter
Biorhythms is an online monthly newsletter that highlights a selected group of relevant, high-impact articles published over the last month in the major journals. Biorhythms is offered as a service to Cellucidate users to assist them as scientists working in cell signaling and regulation, to keep abreast of the most significant developments in the field over the last month. Each online issue has brief, easy to read digests of the selected research articles, with links to the online sources, including where applicable, Cellucidate's own library of biological models.
Raf-MEK-ERK
This book simulates the sequential activation of the Raf/MEK/ERK cascade from the Map Kinase Cascades. The Raf/MEK/ERK cascade is essential part of many RTK induced signaling networks. ERK activation induces transcription which ultimately leads to numerous cellular processes such as growth, division and death. Due to its integral part in vital cell processes, aberrant regulation of this cascade is implicated in many cancers. Numerous drugs are currently under clinical investigation to attempt to inhibit this pathway’s key players ( 2002 S. Karger GmbH, Freiburg).
mTOR
The mTOR cBook gives a general overview of the pathway that mTOR is involved in. It begins from IRS1/2 and goes all the way down to capture the eIF-4E and S6 transcription factors.The model shows how well Cellucidate simulations mimic actual published, literature results. This model can be extended to incorporate various other arms related to Akt’s phosphorylation and can be used to shed light on such hazy areas. It can also be expanded to incorporate the negative feedback loop that is initiated by mTOR’s indirect activation of S6K1.
Simple RTK Model
This book is a simple Cellucidate example that describes the activation of a receptor tyrosine kinase and a downstream kinase.
General Biobricks Framework
This book contains components from the Biobricks catalog, along with models that demonstrate the properties of synthetic systems constructed from these biological modules.
The ErbB Signaling Network
This cBook demonstrates the basal activation and normal ligand-induced activation of the ErbB receptor network and the kinetics of the formation of the various species of ErbB homodimers and heterodimers.
From EGF to Akt
This book explores the effect of cMET levels on Akt activation with low levels of ligand. The Hepatocyte Growth Factor Receptor (or cMET) pathway interacts closely with the EGFR pathway which is implicated in numerous types of cancers.
The Intrinsic Apoptosis Pathway
This cBook describes the intrinsic apoptosis pathway including the mitochondrial apoptosis circuits.
SoS Recruitment
This book explores the different methods of SoS recruitment ("Long Arm" vs. "Short Arm") and therefore induction of the Map Kinase cascades. The Short arm mechanism is initiated by EGFR bind Grb2, which in turn activates Ras directly through SoS binding. While the Long arm mechanism is initiated by EGFR binding Shc, which in turn binds Grb2 and activated Ras directly through SoS binding.
The Role of ErbB2 in Cancer
This cBook demonstrates the basal activation and normal ligand-induced activation of the ErbB receptor network and contrast these situations to the activation of the network that results from the overexpression of ErbB2. It also demonstrates the kinetics of the formation of the various species of ErbB homodimers and heterodimers.
The Canonical Il-13 Pathway
IL-13 (Interleukin 13) is a cytokine that is invovled in mediating inflammatory responses caused by allergies and disease. It sets of the IL-13 pathway (which is related to the IL-4 pathway) and activates species like Jak1, Jak2 and Tyk2. These species then trigger further downstream events that eventually lead to the anti-inflamatory response.
Yeast Pheromone Response
This book describes the pheromone response pathway in Saccharomyces cerevisiae, and includes simulations of receptor and G protein dynamics, as well as of MAPK dynamics.
Ras Stochasticity
This book explores the different methods of Ras regulation and their effect on ERK activation - and therefore initiation of Transcription. Our simulations of the EGFR/Ras/MAPK cascade using the Kappa modeling platform reveal that when EGFR relinquishes its control of Ras, the downstream cascade remains acutely sensitive to the current Ras activation state and that there exists an "activation threshold" above which the cascade is triggered. The results from many Kappa simulations divide approximately evenly between 3 distinct behaviors for the cascade.
The PDGFR-α Pathway
This cBook is a representation of the PDGFR-alpha pathway model from the Pathway Interaction Database (PID - http://pid.nci.nih.gov/PID).
Met Levels and Akt Activation
This cBook explores the effect of cMET levels on Akt activation with low levels of ligand. The Hepatocyte Growth Factor Receptor (or cMET) pathway interacts closely with the EGFR pathway which is implicated in numerous types of cancers. On the receptor level, cMET can bind and dimerize HER3 to activated ErbB family effectors. Further downstream, cMET activates the Akt pathway - also activated by EGFR and heavily implicated in cell survival. Under normal levels of receptors and in the absence of ligand, only a basal level of activating signal reaches Akt. However, when cMET levels are overexpressed which is a common condition in gastric cancer, higher levels of Akt are activated even in the absence of ligand.
The Repressillator
This book contains a model of the "repressilator" synthetic oscillatory network described by Elowitz and Leibler in Nature 2000 Jan 20;403(6767):335-8. The repressilator is comprised of a circuit of three transcriptional repressors and is characterized by an oscillatory behavior - hence the name repressilator.
The Extrinsic Apoptosis Pathway
This book provides a general collation of the extrinsic apoptosis pathway starting with the death receptors. Extrinsic Apoptosis (programmed cell death) is an elegant example of the cell’s harmony between cellular signaling and spatial temporal mechanisms. Due to the important regulatory nature of apoptosis, it is a very heavily regulated mechanism. Intuitively, aberrant regulation in apoptosis can result in numerous types of disease including cancers, when a cell loses its ability to systematically destroy itself the breaks are cut.
Biorhythms is an online monthly newsletter that highlights a selected group of relevant, high-impact articles published over the last month in the major journals. Biorhythms is offered as a service to Cellucidate users to assist them as scientists working in cell signaling and regulation, to keep abreast of the most significant developments in the field over the last month. Each online issue has brief, easy to read digests of the selected research articles, with links to the online sources, including where applicable, Cellucidate's own library of biological models.
Raf-MEK-ERK
This book simulates the sequential activation of the Raf/MEK/ERK cascade from the Map Kinase Cascades. The Raf/MEK/ERK cascade is essential part of many RTK induced signaling networks. ERK activation induces transcription which ultimately leads to numerous cellular processes such as growth, division and death. Due to its integral part in vital cell processes, aberrant regulation of this cascade is implicated in many cancers. Numerous drugs are currently under clinical investigation to attempt to inhibit this pathway’s key players ( 2002 S. Karger GmbH, Freiburg).
mTOR
The mTOR cBook gives a general overview of the pathway that mTOR is involved in. It begins from IRS1/2 and goes all the way down to capture the eIF-4E and S6 transcription factors.The model shows how well Cellucidate simulations mimic actual published, literature results. This model can be extended to incorporate various other arms related to Akt’s phosphorylation and can be used to shed light on such hazy areas. It can also be expanded to incorporate the negative feedback loop that is initiated by mTOR’s indirect activation of S6K1.
Simple RTK Model
This book is a simple Cellucidate example that describes the activation of a receptor tyrosine kinase and a downstream kinase.
General Biobricks Framework
This book contains components from the Biobricks catalog, along with models that demonstrate the properties of synthetic systems constructed from these biological modules.
The ErbB Signaling Network
This cBook demonstrates the basal activation and normal ligand-induced activation of the ErbB receptor network and the kinetics of the formation of the various species of ErbB homodimers and heterodimers.
From EGF to Akt
This book explores the effect of cMET levels on Akt activation with low levels of ligand. The Hepatocyte Growth Factor Receptor (or cMET) pathway interacts closely with the EGFR pathway which is implicated in numerous types of cancers.
The Intrinsic Apoptosis Pathway
This cBook describes the intrinsic apoptosis pathway including the mitochondrial apoptosis circuits.
SoS Recruitment
This book explores the different methods of SoS recruitment ("Long Arm" vs. "Short Arm") and therefore induction of the Map Kinase cascades. The Short arm mechanism is initiated by EGFR bind Grb2, which in turn activates Ras directly through SoS binding. While the Long arm mechanism is initiated by EGFR binding Shc, which in turn binds Grb2 and activated Ras directly through SoS binding.
The Role of ErbB2 in Cancer
This cBook demonstrates the basal activation and normal ligand-induced activation of the ErbB receptor network and contrast these situations to the activation of the network that results from the overexpression of ErbB2. It also demonstrates the kinetics of the formation of the various species of ErbB homodimers and heterodimers.
The Canonical Il-13 Pathway
IL-13 (Interleukin 13) is a cytokine that is invovled in mediating inflammatory responses caused by allergies and disease. It sets of the IL-13 pathway (which is related to the IL-4 pathway) and activates species like Jak1, Jak2 and Tyk2. These species then trigger further downstream events that eventually lead to the anti-inflamatory response.
Yeast Pheromone Response
This book describes the pheromone response pathway in Saccharomyces cerevisiae, and includes simulations of receptor and G protein dynamics, as well as of MAPK dynamics.
Ras Stochasticity
This book explores the different methods of Ras regulation and their effect on ERK activation - and therefore initiation of Transcription. Our simulations of the EGFR/Ras/MAPK cascade using the Kappa modeling platform reveal that when EGFR relinquishes its control of Ras, the downstream cascade remains acutely sensitive to the current Ras activation state and that there exists an "activation threshold" above which the cascade is triggered. The results from many Kappa simulations divide approximately evenly between 3 distinct behaviors for the cascade.
The PDGFR-α Pathway
This cBook is a representation of the PDGFR-alpha pathway model from the Pathway Interaction Database (PID - http://pid.nci.nih.gov/PID).
Met Levels and Akt Activation
This cBook explores the effect of cMET levels on Akt activation with low levels of ligand. The Hepatocyte Growth Factor Receptor (or cMET) pathway interacts closely with the EGFR pathway which is implicated in numerous types of cancers. On the receptor level, cMET can bind and dimerize HER3 to activated ErbB family effectors. Further downstream, cMET activates the Akt pathway - also activated by EGFR and heavily implicated in cell survival. Under normal levels of receptors and in the absence of ligand, only a basal level of activating signal reaches Akt. However, when cMET levels are overexpressed which is a common condition in gastric cancer, higher levels of Akt are activated even in the absence of ligand.
The Repressillator
This book contains a model of the "repressilator" synthetic oscillatory network described by Elowitz and Leibler in Nature 2000 Jan 20;403(6767):335-8. The repressilator is comprised of a circuit of three transcriptional repressors and is characterized by an oscillatory behavior - hence the name repressilator.
The Extrinsic Apoptosis Pathway
This book provides a general collation of the extrinsic apoptosis pathway starting with the death receptors. Extrinsic Apoptosis (programmed cell death) is an elegant example of the cell’s harmony between cellular signaling and spatial temporal mechanisms. Due to the important regulatory nature of apoptosis, it is a very heavily regulated mechanism. Intuitively, aberrant regulation in apoptosis can result in numerous types of disease including cancers, when a cell loses its ability to systematically destroy itself the breaks are cut.