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Sunday, October 28, 2012

Data manager in computational material science

Introduction

Tilde (wwwtilda, ~) is a data manager in cheminformatics and computational material science. The nowadays situation in these disciplines with a plenty of incompatible data formats is rather confusing. Furthermore a new approach to the scientific data verification and exchange is desired because the traditional peer-reviewed journals and their supplementary materials sections do not solve this task properly.
Therefore Tilde aims to simplify data processing and exchanging for the scientists, dealing with popular computer simulation packages in material science (e.g. VASPCRYSTALWIEN2K etc). Now the text outputs of these programs can be collected, and the calculated results therein can be visualized. The example focus is on phonon properties of the crystalline materials: vibrational spectra, band structures, densities of states, vibrational patterns visualization etc.
Moreover Tilde acts as an infrastructure for user's own scripts and applications, organizing them under single hood and assisting to pipe data throughout them. The third-party scripts and programs so could be easily integrated in Tilde with its application programming interface (API).

 Technical details

Tilde is a client-server application. Usually for a client side of such applications one needs a web-browser as a user interface, while a server side resides somewhere remotely in the cloud.
Tilde however lives totally at the user own computer acting as a small local web-server. All user private data are therefore stored securely on a local computer. Tilde web-server generates a website with a snapshot of user calculations and modelling results. This website is protected by operating system and only available to current user, though he or she is able to share some of the results with others (see below). Tilde is written in Python programming language and therefore highly portable, the same code is used on board of Windows, Linux and Apple machines.
Pic. 1. Software architecture (red are supported programming languages, product names and tech standards are underlined)
Tilde is a networking application meaning the different running copies of it can communicate with each other located on different computers over the Internet. So its participants can connect and exchange data, compare their calculations and find out bugs together in modelling programs that they use for own data-mining.
Tilde was inspired by torrents, Skype and jabber applications. Their common feature is a peer-to-peer distributed syndication. So Tilde tries to adopt this idea to a data exchange in a scope of scientific problems, namely, computational modelling in physics and chemistry.

Requirements

The server side of Tilde is written in Python which generally speaking means it is able to run everywhere, on Windows, Unix, MacOS, Symbian computers and others where Python interpreter is implemented. It actually has been tested only on Windows 7, Windows XP and UNIX Debian though.
The client side of Tilde runs in any modern HTML5 web-browser (normally, Google Chrome, Mozilla Firefox or Safari). Flash and Java plugins are not required.

Licensing

Tilde has MIT-license. This means everybody is welcomed to use it for own needs or modify and adopt its source code.

Demo

Demo is actually running on a virtual Linux machine, which was kindly provided by Peterhof Telecommunication Center of St.Petersburg State University

Download

Tilde is a young actively developing project. API and networking features are not completed until now, so the sophisticated users are advised to wait for a stable release. For an early development code summary please refer to the downloads section. Have a look at the flyer therein as well:

Relative projects

Not only Tilde represents the need for a new instrument in scientific data management, manipulation and exchange. For example, other projects are:
Not a secret that the world wide web itself was initiated as a mean of data exchange in the scientific community. The concept of a hyperlink came from scientific publications, being a way to reference the output of other scientists in the field. In this sense the principle of open data, open source scientific code and open standards is crucial. It is declared by an initiative group with a symbolic name Blue Obelisk (http://www.jcheminf.com/content/3/1/37).

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Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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