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Python在生物研究中的应用浅谈
1.
Python 在生物研究中的应用浅谈 Q
Chung
2.
第一篇 目录 蛋白质结构中
python 的应用 基因测序中 python 的应用 复杂科学计算中 python 的应用 模拟生物中 python 的应用 4 1 2 3 四个方面粗浅的总结与现实问题的提出
3.
蛋白质结构分析相关 Py 模块
STRUCTURAL BIOINFORMATICS 结构生物信息学 1 、 PConPy 用于生成二维蛋白质包括空间、距离、氢键分析 2 、 PyRosetta 自定义的结构预测和设计算法,设计实施和示范蛋白质对接算法,蛋白质折叠,循环模型。 3 、 Biskit 一个 py 库,分析大分子结构,分子动力学和蛋白质复合物 4 、 PROVAT 一种蛋白质结构的 Voronoi 镶嵌和复合物的分析工具。
4.
蛋白质结构分析相关 Py 模块
STRUCTURAL BIOINFORMATICS 结构生物信息学 5 、 ProDy 同源的蛋白质,其突变和序列抑制剂分析 6 、 PyETV 一个查看,分析和预测其操纵的重要蛋白质的结构的 pymol 插件 7 、 GimmeMotifs 一个为 ChIP 芯片做管道分析的包, python 实现,可是运行于 linux 下 8 、 PIANA 蛋白质的相互作用和网络分析,预测凝胶蛋白电泳的相互作用,这个非常有用
5.
6.
下游检测产品形式、原理 早早孕试纸条 其原理与结构
受限制于这两条 红色 线上的原料
7.
下游检测关键性要求 需要提高的关键性指标 抗体灵敏度的提高
样本假阳性的降低
8.
上游免疫学原料的优化 小分子单克隆抗体 +
稳定的小分子抗原 高灵敏度 高效价 高亲和力 强特异性
9.
问题分解:抗原表位的分析 Pymol ABC-SysBio
Sarment bio-pathfinder 目前发现能用到的一些 Py 包与插件 两化合物作用 找酶途径 预测最大分区 HMM 的分析 特定模型的选择 参数分析 抗原结构渲染动画 三维结构渲染
10.
问题分解:抗体结构的分析 Pymol 1.
三维结构的渲染和动画软件。高品质的分子三维结构,适合抗原与抗体的研究。 2 所有正式发表的科学论文中的蛋白质结构图像中,有四分之一是使用 Pymol 来制作的。 3.Win 下需要 Python 、 CygWin 、 C++ 、 OpenGL 等支持。 抗原结构渲染与动画 三维结构渲染
11.
问题分解:抗体结构的分析 结构与识别
12.
可能的解决方案 可能解决方案 抗体筛选
Py 写筛选程序, GUI 化的实验室桌面软件辅助筛选(缺乏) 抗原构建 通过 Py 一部分程序(非常缺乏)对抗原结构的分析,合成优异抗原 质量的提升 最终实现灵敏度的提高、假阳性的降低、特异性高、效价高 免疫优化 Py 分析免疫周期中注射量、佐剂量等长期数据,优化免疫方式
13.
基因组相关 Py 模块(探索中)
GENOME ANALYSIS 基因组分析 1 、 Ruffus 一个轻量级的运行计算管道方面的模块 2 、 GenomeDiagram 用于生物序列的可视化的大型基因组,比较基因组 3 、 tCal 基于热力学模型的转录概率计算器,用户可以使用 tCal 建立转录单位,转录或计算概率,或构建基因调控网络 SBML 模型的研究 4 、 Easyfig 一个可视化的基因组比较, BLAST 的比较基因组之间的多个地区,从单基因到整个原核生物染色体,有可视化和交互功能 5 、 PYCHEM 广泛适用于后基因组学科
14.
基因测序相关 Py 模块(探索中)
sequence analysis 序列分析 1 、 Biopython 一个免费的计算分子生物学和生物信息学工具,主要 BLAST ,知名度最高 2 、 BlastAlign 一个使用 BLAST 分析核苷酸序列的包 3 、 TAMO 一个灵活的,面向对象的利用 DNA 转录调控序列图案分析框架
15.
基因测序相关 Py 模块(探索中)
较为知名的 Biopython
16.
基因测序相关 Py 模块(探索中)
较为知名的 Biopython
17.
科学计算相关 Py 模块(探索中)
Numpy- 快速处理数据 Scipy- 数值计算库 Sympy- 符号运算帮手 M atplotib — 绘制图和表
18.
科学计算相关 Py 模块(探索中)
19.
生物模拟相关 Py 模块(探索中)
PHYLOGENETICS 系统发生学 +SYSTEMS BIOLOGY 系统生物学 1 、 PySCeS 蜂窝系统建模 2 、 PyNAST 基于序列的微生物生态群落分析 3 、 DendroPy 3.7.1 阅读,写作,模拟,处理和(系统发育)和人物进化树的操作:系统发育和进化的一个计算 Python 库。
20.
在生物模拟系统中的应用 主要用于对生物细胞等大型复杂系统进行建模,模拟和分析,技术路线是在硅片上模拟重建生物现象,能够精细地模拟全细胞所必要的理论、技术和软件平台开发支持的国际研究项目。 从
E-Cell 3.x 开始还提供了 Python 编程语言的标准 。 E-Cell 3 核心模拟软件是一组 Python 语言解释器的扩展模块,用 c++/c/python 写的。利用 E-Cell 模型描述语言 EML ( Model description Language), XML 的子集 , 描述模型。为了能够跨平台交换模型,也正在开发对系统生物学标签语言 SBML ( Systems Biology Markup Language) 的支持。 一个例子:虚拟原核细胞模型 -E-Cell
21.
在生物模拟系统中的应用 虚拟原核细胞模型 E-Cell
硅片上的 E-cell 模型
22.
在生物模拟系统中的应用 虚拟原核细胞模型 E-Cell
127 个基因的自维持细胞 SSC 模型
23.
在生物模拟系统中的应用 1 、还有美国建立的真核细胞钙转运的模型
2 、 NIH 和 DOE 筹建关于细胞信息传递和生物利用能量的虚拟细胞
24.
其他有意义的模块 CompariMotif
CARPET PseudoPipe Selenoprofiles MSPocket ARIA SCAssign QPRIMER 。。。。。。 其他有意义的模块
25.
一些有意义的杂志期刊 Bioinformatics BMC
Bioinformatics Plos Comput Biol J.Computational Biolog NUCLEIC ACIDS RES Genome Biol Nat Methods & Nat Biotech’ Bioinformatics Sections
26.
Q Chung 2011.4.17
Thank You!
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