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| [[Image:Pano1.jpg|750px]] | | My name is [http://www3.abhishek-tiwari.com/ Abhishek Tiwari] and I am PhD student in Bioengineering at [http://www.abi.auckland.ac.nz/uoa/ Auckland Bioengineering Institute], the [http://www.auckland.ac.nz/ University of Auckland]. I am condcuting my doctoral research on modelling of hormone dynamics. This wiki is the new home of my PhD research activities and it will provide models, results, experiments, or any other insights related to the project. I also maintain the [http://www.abhishek-tiwari.com/ Fisheye Perspective] blog which aggregates my random thoughts and speculations about science, systems biology, synthetic biology and technology. |
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| [[Abhishek Tiwari | <font face="trebuchet ms" style="color:#ffffff"> '''Home''' </font>]]
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| [[Abhishek Tiwari:Contact | <font face="trebuchet ms" style="color:#ffffff"> '''Contact''' </font>]] | |
| [[Abhishek Tiwari:iCODONS | <font face="trebuchet ms" style="color:#ffffff"> '''iCODONS''' </font>]]
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| [[Abhishek Tiwari:Reprints | <font face="trebuchet ms" style="color:#ffffff"> '''Publications''' </font>]]
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| [[Abhishek Tiwari:Research | <font face="trebuchet ms" style="color:#ffffff"> '''Research''' </font>]] | |
| [[Abhishek Tiwari:Projects | <font face="trebuchet ms" style="color:#ffffff"> '''Projects''' </font>]]
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| [[Abhishek Tiwari:Softwares | <font face="trebuchet ms" style="color:#ffffff"> '''Softwares''' </font>]]
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| [[Abhishek Tiwari:Links | <font face="trebuchet ms" style="color:#ffffff"> '''Links''' </font>]]
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| | ==Project content== |
| | *Table of content-[[Modelling Hormone Dynamics]] |
| | *Publications-[[Manuscripts Modelling Hormone Dynamics]] |
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| | ==Quick Links== |
| | | *[[Curated HPA-Axis Models]] |
| =Welcome to webpage of Abhishek Tiwari= | | *[[Modelling ACTH-induced steroidogenesis]] |
| | | *[[Multicellular simulation using CellML]] |
| The current focus of my research is the application of computational methods and tools to solve biological problems of fundamental significance. More details can be found in [[Abhishek Tiwari:Research|Research]] section. Currently I am working as Research Associate with Informatics Group at GVK Biosciences. I am also a member of Prof Gautam R. Desiraju Research Group at School of Chemistry at University of Hyderabad.
| | *[[Hormone Dynamics of HAC15/Y1 Cells]] |
| | | *[http://openwetware.org/wiki/OpenWetWare:Information_management/PubgetNotes Referring DOI and PMID] |
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| ==Workflow technology, Cheminformatics and Drug Discovery==
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| [[Image:Data_Pipelining.jpg]]
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| Workflow technology is a mechanism to integrate data, application and services. Workflow technology enables scientist to dynamically construct their own research protocol for scientific analytics and decision making by connecting various resources and software applications together in an innovative way. Workflow technology is being increasingly applied in discovery informatics to organize and analyze data. SciTegic's Pipeline Pilot is a one of the chemically intelligent implementation of a workflow technology known as data pipelining. It allows scientists to construct and execute workflows using components that encapsulate many cheminformatics based algorithms.
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| Workflow technology is generic so analytics work flow can be built for any areas like gene expression analysis, sequence analysis, proteomics, system biology and so on. Workflow technology provides an interface where software from different vendors can assemble according to scientific requirement.
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| [[Abhishek Tiwari:Workflow technology|Read More]]
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| == Chemical Informatics or Cheminformatics Toolkit Programming ==
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| "Any idiot can stand up and say that virtual screening doesn't work. It takes real brains to show how to improve it!" - Mark McGann
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| Currently a lot of toolkits (Daylight Toolkit, Chemaxon Toolkit, OpenEye Toolkit, MOE SVL, Accord, CDK, JOELib etc) are available from different vendors and organization. Most of them are equally good but choice may vary based on user prospective. I will try to give a summarized overview of some commonly used Chemical Informatics Toolkits. For academics user Chemaxon JChem (which is free for academic user) and Open Source Toolkits like CDK and JOELib will be a better choice. If your budget permits then you can use Daylight, Accord , OpenEye, MOE SVL or any other depending on your needs but Chemaxon and MOE are low budget high quality options.
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| [[Abhishek Tiwari:Chemical Informatics Toolkits|Read More]]
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| == In News == | |
| [[Image:3dcomplex.PNG]] http://www.3dcomplex.org/
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| '''''PLoS Computational Biology''''' Volume 2 | Issue 10 | OCTOBER 2006
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| *'''3D Complex: a Structural Classification of Protein Complexes''' | |
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| '''Synopsis'''
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| Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physico-chemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here Emmanuel D Levy,etl. propose the first hierarchical classification of whole protein complexes of known three-dimensional structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows non-redundant sets to be derived at different levels of detail. This reveals that between one half and two thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits, and find that they form a small number of arrangements compared to all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, they identified many possible errors in quaternary structure assignments. Our classification, available as a database and web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.
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| '''TreeDyn'''[[Image:logotreedyno.gif]] http://www.treedyn.org/
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| '''''BMC Bioinformatics''''' Volume 7 | OCTOBER 2006
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| *'''TreeDyn: towards dynamic graphics and annotations for analyses of trees'''
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| '''Synopsis'''
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| TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.TreeDyn is using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.
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| = Latest Sections =
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| * [[Abhishek Tiwari:BioCreAtIvE II|BioCreAtIvE II]]
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| * [[Abhishek Tiwari:Hot Computational Biology Papers-By Category|Hot Computational Biology Papers-By Category]] | |
| * [[Abhishek Tiwari:Links|Hot Computational Biology Links-By Category]] | |
| * [[Abhishek Tiwari:Flashback|Flashback]] | |
| * [[Abhishek Tiwari:INTERACTOMICS_NETWORKS|Images From Biological Interaction Network]] | |
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