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Part 1: Document Description
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Citation |
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Title: |
NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
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Identification Number: |
doi:10.21979/N9/IP6DBD |
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Distributor: |
DR-NTU (Data) |
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Date of Distribution: |
2017-09-19 |
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Version: |
1 |
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Bibliographic Citation: |
Zheng, Jie, 2017, "NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential", https://doi.org/10.21979/N9/IP6DBD, DR-NTU (Data), V1 |
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Citation |
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Title: |
NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential |
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Identification Number: |
doi:10.21979/N9/IP6DBD |
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Authoring Entity: |
Zheng, Jie (Nanyang Technological University) |
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Software used in Production: |
(To be provided) |
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Grant Number: |
AcRF Tier 1 Seed Grant on Complexity RGC2/13 |
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Grant Number: |
AcRF Tier 1 Grant 2015-T1-002-094, RG120/15 |
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Distributor: |
DR-NTU (Data) |
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Access Authority: |
Zheng, Jie |
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Depositor: |
Cheng, Wei Yeow |
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Date of Deposit: |
2017-08-26 |
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Holdings Information: |
https://doi.org/10.21979/N9/IP6DBD |
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Study Scope |
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Keywords: |
Computer and Information Science, Computer and Information Science, Open-source software tool, Application, Quantitative modeling, Quantitative visualization, Waddington’s epigenetic landscape |
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Abstract: |
<h3>About NetLand</h3> <p>NetLand is a software for quantitative modeling and visualization of Waddington’s epigenetic landscape.</p> <p>NetLand is intended for modeling, simulation and visualization of gene regulatory networks (GRNs) and their corresponding quasi-potential landscapes. Users can import models of GRNs from a file (e.g. TSV, SBML format etc.), and manually edit the network structure. Then, NetLand will automatically encode differential equations for the kinetics of transcriptional regulations. The computational model will be used to simulate the dynamics of the input networks. Model equations and parameters can be easily modified.</p> <p>To display the 3D landscape for a network of more than two genes, NetLand allows users to either choose two marker genes, or project to a latent space using a dimensionality reduction method called GPDM (Gaussian process dynamical model). Therefore, NetLand can provide a global picture of cellular dynamics for a user-specified GRN. Although we designed the NetLand software originally for modeling stem cell fate transitions, it can be also used to study other cellular phenotypes, such as cancer cell death, cellular ageing, etc.</p> <h3>Download</h3> <p>The software NetLand is written in Java, with a graphical user interface (GUI). The <a href="https://github.com/NetLand-NTU/NetLand/blob/master/NetLand_manual.pdf">user manual</a> contains detailed instruction about installation and basic usage. It also includes running time and memory usage assessment and case studies.</p> <p> <p style="color:#6f2a11 ;">The source code and additional resources are available for downloading in this dataset record. They can also be downloaded at <a href="https://github.com/NetLand-NTU/NetLand/">Github</a>.</p> </p> <p></p> </body> |
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Kind of Data: |
Software |
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Kind of Data: |
Source code |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Identification Number: |
10.1093/bioinformatics/btx022 |
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Bibliographic Citation: |
Guo, J., Lin, F., Zhang, X., Tanavde, V.,& Zheng, J. NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential. Bioinformatics 2017; 33 (10): 1583-1585. |
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Citation |
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Identification Number: |
10356/85842 |
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Bibliographic Citation: |
Guo, J., Lin, F., Zhang, X., Tanavde, V.,& Zheng, J. NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential. Bioinformatics 2017; 33 (10): 1583-1585. |
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Label: |
.gitignore |
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Notes: |
text/plain; charset=US-ASCII |
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Label: |
GPDM.zip |
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Notes: |
application/zip |
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Label: |
lib.zip |
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Notes: |
application/zip |
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Label: |
LICENSE |
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text/plain; charset=US-ASCII |
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main.jar |
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Notes: |
application/java-archive |
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NetLand_manual.pdf |
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application/pdf |
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netland.wmv |
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video/x-ms-wmv |
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README.docx |
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Text: |
Converted from README.md |
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Notes: |
application/vnd.openxmlformats-officedocument.wordprocessingml.document |
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Label: |
README.md |
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Notes: |
text/plain; charset=UTF-8 |
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Label: |
runNetLand.bat |
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application/x-msdownload |
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runNetLand.sh |
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Notes: |
application/x-sh |
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saved results.zip |
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application/zip |
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src.zip |
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application/zip |
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toy models.zip |
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Notes: |
application/zip |