Charlie’s path to dEAth

这个视频，是Oakwood公司的宣传用Presentation。说的是他们在为Tennessee州的法庭Court Data提供数据服务时，是怎样通过MS SQL Server 2005的Analysis Service等产品取得的成功。内容很不错，包括了

• Report Service介绍。
• OLAP的概念，OLAP为何而来。
• 为什么需要ETL(Extraction, Transformation, Loading) 及 SSIS (Integration Service)。
• Analysis Service中Cube的组成和概念。其中对Star Schema中Fact table, Dimension table, Dimension, Measure的介绍，比微软官方产品介绍和MSDN中的文章都要精要直观。
• 很重点地介绍了Excel作为SSAS客户端的情况。了解Excel中Pivot table，对SSAS基础体系结构的理解很有好处。
• 提了一下SSAS中数据挖掘的功能。
• 侧面介绍了美国司法体系中的开放性。
• 当然，还有对Oakwood的blahblah…

在试图了解一项技术的基本概念，想知道它能做什么的时候，一个比较快捷的方法就是，去Youtube上搜索视频，去Google上搜索PPT。

Filed by charlie at 10:47 pm under Engineer, resource
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SMILES on Wikipeida

The original SMILES specification was developed by Arthur Weininger and David Weininger in the late 1980s. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc.

it also has a wide base of software support with extensive theoretical (e.g., graph theory) backing.

A common application of Canonical SMILES is for indexing and ensuring uniqueness of molecules in a database.

In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree.

SMARTS is a modification of SMILES that allows, in addition to the SMILES elements, the specification of wildcard atoms and bonds. This is used in specifying search structures and is widely used in chemical database search applications.

Improved SMILES Substructure Searching , by Daylight

Daylight Theory Manual - Covering general information on representing molecules and an in-depth discussion of SMILES^TM, SMARTS^®, SMIRKS^®, fingerprints, THOR database concepts, and Merlin analysis <html, pdf>

SMARTS - A Language for Describing Molecular Patterns

Fingerprints - Screening and Similarity

OpenBabel, including Implementation of Daylight SMARTS molecular matching syntax

makefp is a command line program to compute hashed path fingerprints from input smiles, or other file formats such as sdf or mol files.

Checkmol is a command-line utility program which reads molecular structure files in different formats (see below) and analyzes the input molecule for the presence of various functional groups and structural elements.

Search by Functional groups

PubChem Similar Searches search allows you to find similar chemical structures to the provided query. Similarity is measured using the Tanimoto equation and a binary fingerprint computed for every structure in the PubChem Compound database. This fingerprint consists of a series of chemical substructure “keys”. Each key denotes the presence or absence of a particular substructure in a molecule. The fingerprint does not consider variation in stereochemical or isotopic information. Collectively, these binary keys provide a “fingerprint” of a particular chemical structure valence-bond form.

PubChem Substructure search allows you to locate chemical structures that contain the particular connectivity and valence bond pattern that you provide in your query. For example, a substructure search of ethanol (SMILES: OCC) would return, among others, acetic acid (SMILE: OC(=O)C), since ethanol is a substructure of acetic acid.

OpenEye software

Roll Your Own Chemical Database With Free Components

Creating a Web-based, Searchable Molecular Structure Database Using Free Software

How to create a web-based molecular structure database with free software, a fine presentation to read.

Filed by charlie at 4:28 pm under Engineer, chemoinformatics, resource
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下载地址:rapidshare
解压密码:gigapedia

来源: http://rapidsharebooks.blogspot.com/2007/03/chemoinformatics-theory-practice.html

Chemoinformatics: Theory, Practice, & Products
Pages:295

Chemoinformatics:
Theory, Practice & Products covers theory, commercially available
packages and applications of Chemoinformatics. Chemoinformatics is
broadly defined as the use of information technology to assist in the
acquisition, analysis and management of data and information relating
to chemical compounds and their properties. This ranges from molecular
modelling, to reactions, to spectra, to structure-activity
relationships associated with chemicals. Computational scientists,
chemists, and biologists all rely on the rapidly evolving field of
Chemoinformatics. Chemoinformatics: Theory, Practice & Products is
an essential handbook for determining the right Chemoinformatics method
or technology to use. There has been an explosion of new
Chemoinformatics tools and techniques. Each technique has its own
utility, scope, and limitations, as well as meeting resistance to use
by experimentalists. The purpose of Chemoinformatics: Theory, Practice
& Products is to provide computational scientists, medicinal
chemists and biologists with unique practical information and the
underlying theories relating to modern Chemoinformatics and related
drug discovery informatics technologies.

The book also provides
a summary of currently available, state-of-the-art, commercial
Chemoinformatics products, with a specific focus on databases,
toolkits, and modelling technologies designed for drug discovery. It
will be broadly useful as a reference text for experimentalists wishing
to rapidly navigate the expanding field, as well as the more expert
computational scientists wishing to stay up to date.

It is
primarily intended for applied researchers from the chemical and
pharmaceuticalindustry, academic investigators, and graduate students.

Filed by charlie at 10:22 pm under chemoinformatics, resource
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自由、免费是否即意味着滥用？自由不受管制的资源可以放大邪恶的力量，绝对的自由化能产生灾难。

Filed by charlie at 10:21 pm under resource
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