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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:About | <font face="trebuchet ms" style="color:#ffffff"> '''About''' </font>]] | |
| [[Abhishek Tiwari:Resources| <font face="trebuchet ms" style="color:#ffffff"> '''Resources''' </font>]]
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| [[Abhishek Tiwari:Projects | <font face="trebuchet ms" style="color:#ffffff"> '''Research & Projects''' </font>]]
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| [[Abhishek Tiwari:Softwares | <font face="trebuchet ms" style="color:#ffffff"> '''Softwares''' </font>]] | |
| [[Abhishek Tiwari:Reprints | <font face="trebuchet ms" style="color:#ffffff"> '''Publications''' </font>]]
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| [[Abhishek Tiwari:Links | <font face="trebuchet ms" style="color:#ffffff"> '''ImpLinks''' </font>]]
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| [[Abhishek Tiwari:Contact | <font face="trebuchet ms" style="color:#ffffff"> '''Contact''' </font>]] | |
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| =Welcome to web page of Abhishek Tiwari=
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| Welcome to my web page. You will get a lot of technical as well as inspirational stuff on my OpenWetWare page. Now is the time to stop believing, and begin to understand. We are here to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.
| | ==Project content== |
| | *Table of content-[[Modelling Hormone Dynamics]] |
| | *Publications-[[Manuscripts Modelling Hormone Dynamics]] |
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| '''''Everyone wants to be appreciated, so if you appreciate someone, don't keep it a secret.'''''
| | ==Quick Links== |
| | | *[[Curated HPA-Axis Models]] |
| =Conferences and Events In News= | | *[[Modelling ACTH-induced steroidogenesis]] |
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| | *[[Multicellular simulation using CellML]] |
| <a href="http://www.iscb.org/ismbeccb2007/"><img src="http://www.plosjournals.org/images/banners/f_ism_isc_01.gif" alt="ISMB/ECCB 2007" border="0"></a>
| | *[[Hormone Dynamics of HAC15/Y1 Cells]] |
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| | *[http://openwetware.org/wiki/OpenWetWare:Information_management/PubgetNotes Referring DOI and PMID] |
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| '''ISMB/ECCB 2007'''
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| The Fifteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) will be held jointly with the Sixth European Conference on Computational Biology (ECCB 2007) in Vienna, Austria on July 21-25, 2007. (http://www.iscb.org/ismbeccb2007/)
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| '''WABI 2007'''
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| The Workshop on Algorithms in Bioinformatics (WABI) 2007 will be hosted by University of Pennsylvania from Sep 08, 2007 through Sep 09, 2007. (http://www.wabi07.org/index.htm)
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| '''Rocky '07'''
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| ISCB is sponsoring the fifth Rocky Mountain Bioinformatics Conference (Rocky '07) in Snowmass/Aspen, Colorado from November 30 - December 2, 2007. (http://www.iscb.org/rocky07/index.html)
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| <a href="http://psb.stanford.edu/"><img src="http://www.plosjournals.org/images/icons/t_hom_mar_15.gif" alt="PSB 2008" border="0"></a>
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| '''PSB 2008'''
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| The Pacific Symposium on Biocomputing (PSB) 2008 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance.(http://psb.stanford.edu/)
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| You can get more information about upcoming Confrences and Events related to Computaional Biology
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| *ISCB Event Board http://www.iscb.org/events/event_board.php | |
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| =Top Hits=
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| =Green Apple=
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| ==Applications of Workflow technology in Cheminformatics ,Bioinformatics 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 Toolkits==
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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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| ==Bioinformatics Toolkits ==
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| As compared to Chemistry and Chemoinformatics where a lot of commercial as well as open source toolkits are available Bioinformatics has very few options. Most of toolkits are specialized in Sequence manipulations and Databases access related and they are not very diverse. Some major toolkits are Geneious API,BioPerl API,BioJava API,BioPython API, Bioconductor, Mathworks Bioinformatics Toolbox,MBT,NCBI Toolkit and many more. At this moment none of these toolkits are complete and mostly they have some specialized applications.
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| [[Abhishek Tiwari:Bioinformatics Toolkits|Read More]] | |
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| ==Hot Computational Biology Papers==
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| [[Abhishek Tiwari:Hot Computational Biology Papers-By Category|Hot Computational Biology Papers]] is one of the most highlighted sections of my Open Wetware page. Section provides synopsis and comments on the selected article related to computaional biology. Readers are also invited to comment and modify the section.
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| ==Using SOAP/WSDL to access the Biological/Bioinformatics Databases==
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| SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/TR/wsdl) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. When large amounts of data need to be retrieved and analysed, this often proves to be tedious and impractical. Today, biological databases are large collections of data that are relatively difficult to maintain outside the centres and institutions that produce them. These data are traditionally accessed using browser-based World Wide Web interfaces.
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| [[Abhishek Tiwari:SOAP/WSDL based webservices for Biological Databases|Read More]]
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| <a href="http://www.iscb.org/"><img src="http://iscb.org/images/index_r3_c1.gif" alt=" The International Society for Computational Biology (ISCB)" border="0"></a>
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