P*********y
发帖数: 310 | 1 I think if the two sbml models all comply with the sbml standard very
strictly, they should be easily merged in a third platform.
The potentially problems are that many sbml models have their own specific
codes embedded sometimes, which may screw up the merging process.
But in theory, if you can import both sbml models into a third platform and
run them individually, I don't see why you can't merge them by just copy/
paste and then patch up with equation terms that describe the linkage
between v |
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z***0
发帖数: 238 | 2 上GOOGLE看看SBML的MANNUAL吧。
最大的优势是：很多现成的MODELS, FOR SIGNAL TRANSDUCTION PATHWAY OR METABOLIC
NETWORKS，可以从SBML的数据库中获取；还有，这些SBML MODEL可以直接在一些分析
软件上使用，比如FLUX ANALYSIS的COBRA；它的RATE 能够用任何形式的FUNCTIONS来表
达；可以直接输入文字形式的REACTION，程序自动辨认其中的STATE VARIABLES。不好
的地方，程序一般比较长，不好DEBUG，而且对于一些系统分析方法如SENSITIVITY
ANALYSIS不好编程，对比MATLAB来说。 |
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A**********e
发帖数: 3102 | 3 这套东西看着已经成了事实标准了，无论是模型库还是模拟软件的支持都很具规模，就
是不知道通用性怎么样，比如说，从两个不相关的组得到的 SBML 模型，用第三方的
GUI 给结合起来，到底能不能快速做出一个新的模型？还是依然需要回到底层重新自己
写 codes？ |
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j***l
发帖数: 100 | 4 谁来科普一下，经常听到SBML，但从来没有用过，它的最大优势是什么？比Matlab或
Mathematica
好用么？ |
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P*********y
发帖数: 310 | 5 The basic idea is that sbml tries to make models portable and exchangeable
between different programming platforms.
It is obvious that models coded in MatLab can't be run in Mathematica, and
vice versa. And there are almost hundreds of other programming/simulation
languages facing similar problems if we want to reuse the model under a
platform different from the one where the model is initially developed.
But we do know that a biological model has commonalities. You have to have (
1) initial con |
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s******a
发帖数: 252 | 6 It's just XML. The best part is a common format for data exchange.
Given the solid support for XML in many modern languages, it is easy to
parse even without specific SBML tools.
When I used libsbml version 3.2 to do a project, I noticed some problems in
the implementation. Well, I just wanted to finish my project. Now, as I look
at libsbml 4.0, they seem to have fixed the problems. However, the API has
changed. Guess what, my code is now broken :-( |
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P*********y
发帖数: 310 | 7 SBML is not a proprietary code format owned by anyone. It is a biological
modeling standard developed by a consortium.
I don't think anyone actually writes the sbml code by himself - it will be
extremely tedious and error-prone. These days people usually build their
models using a particular simulation platform,and if the platform supports
sbml, it will generate the sbml code automatically for you. Simulation
platforms that support sbml - either importing or exporting sbml or both -
can be found |
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x********u
发帖数: 430 | 8 【 以下文字转载自 SysBio 俱乐部 】
发信人: xiaoyaoyou (逍遥游), 信区: SysBio
标 题: 请教如何将libSBML绑定到Matlab或者其他编译工具上，谢谢！
发信站: BBS 未名空间站 (Mon Jul 12 22:51:17 2010, 美东)
在安装SBML toolbox之前要把libsbml 绑定到matlab或者C+或者Java等编译软件。本人
用WINDOWS XP系统，Matlab版本为7.1。每次按照说明安装libsbml，运行时总会有
install_Win32出错。如果直接安装sbml toolbox则会弹出 Binding not installed.
SBMLToolbox requires that the MATLAB binding of libSBML is installed.
我是一个计算机语言白吃，请问高手如何解决这一问题。谢谢！ |
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x********u
发帖数: 430 | 9 【 以下文字转载自 Biology 讨论区 】
发信人: xiaoyaoyou (逍遥游), 信区: Biology
标 题: 请教如何将libSBML绑定到Matlab或者其他编译工具上，谢谢！ (转载)
发信站: BBS 未名空间站 (Mon Jul 12 22:57:26 2010, 美东)
【 以下文字转载自 SysBio 俱乐部 】
发信人: xiaoyaoyou (逍遥游), 信区: SysBio
标 题: 请教如何将libSBML绑定到Matlab或者其他编译工具上，谢谢！
发信站: BBS 未名空间站 (Mon Jul 12 22:51:17 2010, 美东)
在安装SBML toolbox之前要把libsbml 绑定到matlab或者C+或者Java等编译软件。本人
用WINDOWS XP系统，Matlab版本为7.1。每次按照说明安装libsbml，运行时总会有
install_Win32出错。如果直接安装sbml toolbox则会弹出 Binding not installed.
SBMLToolbox requires that the MATLAB b |
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A**********e
发帖数: 3102 | 10 最近查了些 SBML 的 model，想用 C++ 来把 MathML 格式的 ODE/DAE 抽出来，或者把
自己的 ODE/DAE 用 C++ 通过 libSBML 直接写成 SBML，发现这个 MathML 的语法很惊
人啊。不知道有没有现成的 interface 可以直接写？ |
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P*********y
发帖数: 310 | 11 I wonder how big your model is? If small, why don't you just code it up in
an sbml-supporting platform and generate the sbml automatically? |
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x********u
发帖数: 430 | 12 在安装SBML toolbox之前要把libsbml 绑定到matlab或者C+或者Java等编译软件。本人
用WINDOWS XP系统，Matlab版本为7.1。每次按照说明安装libsbml，运行时总会有
install_Win32出错。如果直接安装sbml toolbox则会弹出 Binding not installed.
SBMLToolbox requires that the MATLAB binding of libSBML is installed.
我是一个计算机语言白吃，请问高手如何解决这一问题。谢谢！ |
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n*****a
发帖数: 2802 | 13 电视难道不是放在family room里的吗？
living room放电视，有点怪。
sbml |
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A**********e
发帖数: 3102 | 16 我考考你：这个 bbs 上一共有多少河马？ :) |
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a****o
发帖数: 1786 | 17 only 2.
The real one and all others. |
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s*****o
发帖数: 26 | 18 我以前实验室有人做这个，其实还没有到这一步。毕竟建模是个艺术活，没法完全技术
标准话。不同模型的对象和风格不
一样。他们现在还是想先从标准做起。 |
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z***0
发帖数: 238 | 19 SBML is not that difficult to learn. Try a simple model and you can feel
that. You don't need to buy a very good computer to run linux. Just a dual-
core computer is good enough if you don't run nonlinear programming.
(
language. |
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P*********y
发帖数: 310 | 20 Should be a nice chapter although the language will need some polishing.
How come I have the feeling that CellML is either phasing out or merging
with SBML?
explosive
and |
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b*****l
发帖数: 9499 | 21 多谢多谢。头大这个语言问题啊。。。
嗯，考虑只重点介绍 SBML，CellML 就略过好了。。。
提供
increases |
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