生物 生物信息学

2009年1月11日星期日

生物信息学书籍推荐 Bioinformatics for Dummies

Author: Jean-Michel Ph. D. Claverie, Cedric Ph.D. Notredame, Jean-Michel Claverie, Cedric Notredame
Edition: 1st
Manufacturer: For Dummies
Number Of Items: 1
Number Of Pages: 432

Bioinformaticsthe process of searching biological databases, comparing sequences, examining protein structures, and researching biological questions with a computeris one of the marvels of modern technology that can save you months of lab work. And the most amazing part is that, if you know how, you can use highly sophisticated programs over the Internet without paying a dime and sometimes, without installing anything new on your own computer. All you need to know is how to use these technological miracles.

Thats where Bioinformatics For Dummies comes in. If you want to know what bioinformatics is all about and how to use it, without wading through pages of computer gibberish or taking a course full of theory, this book has the answers in plain English. Youll find out how to

  • Use Internet resources
  • Understand bioinformatics jargon
  • Research biological databases
  • Locate the sequences you need
  • Perform specific tasks, step by step

Written by two experts who helped develop the science, Bioinformatics For Dummies is all about getting things done. If youre just getting your feet wet, start at the beginning with a quick review of those necessary parts of microbiology and an overview of the tools available. If you already know what you want to do, you can go directly to a chapter that shows you how. Get the lowdown on

  • Researching and analyzing DNA and protein sequences
  • Gathering information from all published sources
  • Searching databases for similar sequences and acquiring information about gene functions through sequence comparisons
  • Producing and editing multiple sequence comparisons for presentation
  • Predicting protein structures and RNA structures
  • Doing phylogenetic analysis

With an Internet connection and Bioinformatics For Dummies, youll discover how to peruse databases that contain virtually everything known about human biology. Its like having access to the worlds largest lab, right from your desk. This book is your lab assistant one that never takes a day off, never argues when you ask it for help, and wont demand a benefits package.

2009年1月10日星期六

CSB 2009:全球第八届计算系统生物学会议

When: Aug 10, 2009 - Aug 13, 2009
Where: Stanford University
Submission Deadline: Mar 15, 2009
Notification Due: May 4, 2009
Final Version Due: May 25, 2009
link: http://www.csb2009.org/

2009年1月9日星期五

分子图形软件——RasMol

RasMol 是一种分子图形软件,可用于蛋白质,核酸及一些小分子物质的可视化。可以跨平台运行于linux,unix,windows,apple,vsm等系统上。

RasMol 可以读取分子的坐标数据,然后交互式,多模式地显示出来。

(图片已删)
图示为DEOXY HEMOGLOBIN (A-GLYGLYGLY-C:V1M,L29W; B,D:V1M)

在生物化学中,或许我们对血红蛋白有个很抽象的了解,通过RasMol,我们可以从多个角度观看其各亚基的结构与位置。如图所示(数据来自pdb),可以看出血红蛋白四个亚基(1,2,3,4)的结构(a螺旋为主)及其内部的疏水区域(5)。并且可以通过改变视角和显示模型对血红蛋白有个更加直观的认识。

详情参见:www.rasmol.org

linux生物信息学发行版

linux本身作为一种开源软件,里面有了丰富的生物信息学工具。
也因此有了应用于各个不同领域的发行版本。下面的版本,集成了生物信息学的很多工具,可以方便的建立生物信息学的工作平台。
下载地址:http://www.mininova.org/tor/2147450
详见www.opendiscovery.org.in

ubuntu中的origin——qtiplot

由于要用的origin,切换的window中比较不方便,故找了下linux中的作图软件。
常用的似乎有gnuplot,但是这是基于命令行的,对我来讲似乎还要求高了点。
所以找了下qtiplot,界面看了下,和origin差不多。

下面是其的一点特性(大概翻译一下):
  • QtiPlot is cross-platform: it works on all systems supported by Qt, including Windows, Linux/Unix and Mac OS X systems.(跨平台,支持windows,linux,mac)
  • QtiPlot is fully scriptable via Python, which gives you the possibility to use powerfull existing scientific tools, such as SciPy, thus bringing unlimited data analysis power.(支持python,这样可以带来更强大无限制的数据处理,在origin 中是对origin c支持,也是刚接触origin的,因此当时也眉宇用到origin c进行扩展之类的)
  • OpenGL based 3D plotting: height maps, user defined functions and parametric surfaces.(3d作图基于OpenGL)
  • Publication quality 2D plots: Error Bars, Multilayer Plots, Bar Plots, Pie Plots, Vector Plots, Contour and Image Plots.(发表质量的2D作图效果)
  • Statistical Plots: Box/Whiskers Diagramms, Histograms.(统计作图)
  • Easy export of plots to vector formats (EPS, PS, PDF, SVG) and to various raster image formats (BMP, JPG, PNG, TIFF etc ...)(能够很容易的导出图形,保存为矢量或者是点状)
  • Powerful and versatile spreadsheets and calculations in column-logic.(强大的表和列的逻辑计算功能)
  • Easy ASCII-Import/Export of single or multiple files.(可以很容易导出为ASCII文件)
  • Linear and nonlinear curve fitting with weighting and estimation of statistical errors of the fit-parameters. The accuracy of QtiPlot can be verified with the Statistical Reference Datasets Project of the National Institute of Standards and Technology (NIST).(线性和非线性拟合)
  • Multi-peak fitting with Gaussian and Lorentzian peak profiles.(峰拟合)
  • Built-in data analysis routines: statistics, sorting, FFT, data smoothing (Savitzky-Golay, FFT smoothing, and moving window average), data filtering (low/high/band pass and band block filters), convolution/deconvolution, correlation, interpolation, numerical integration/differentiation, etc...
  • Matrices optimized for image analysis.(内置的强大的数据分析)
  • Templates support: all the settings for plots (2D/3D), tables and matrices can be saved to ASCII files and restored later on for a fast editing process.(支持模板)
  • Project files based on folders, a powerful project explorer with extensive built-in features: drag and drop, searching facilities, etc...(基于项目的文件夹管理)
  • Import of Origin 7.5 files.(能够导入origin 7.5的文件)

具体参见http://soft.proindependent.com/qtiplot.html

biopython 生物信息学的强有力的工具

biopython,里面有很多生物信息学的工具.
而python的很多特性,开源,跨平台,已经广泛的应用于各个领域。