微生物学与系统生物学发展

系统生物学是研究生物网络系统的科学,从基因调控网络到细胞、组织和生物体网络,阐明生物系统的构成、动力学及控制方式。系统生物学是以假说驱动的研究策略,在综合现有数据的基础上构建系统模型,根据模型提出可以检测的假说,并设计实验以验证假说,根据实验结果再修正模型,不断重复以得到正确的系统模型。在系统生物学的发展中,细菌作为一个很好的模式生物,将起到重要作用。系统生物学的发展不仅依赖于新技术的发明和应用,更有赖于以新的思路去培养新一代的生物学家。     

谈高考试题中的实验设计

实验能力是一种综合能力,目前高考虽然还不具备考查考生的实验操作能力,但非常重视实验内容的考查,如实验原理、实验目的、实验程序、实验现象和实验结论等内容的分析以及实验步骤的设计。其中, 实验步骤的设计,要求学生具备较高水平的综合能力。需要学生动用已学过的多种理论知识,结合实验操作的实践经验,经过周密的分析、逻辑的推理才能做出一个科学、合理的实验设计方案。对照实验设计是一个常考常新的题。笔者根据自己近20年的教学实践经验,总结出了对照实验设计“三步曲”法:第1 步:“共性处理”,第2步:“变量处理”,第3步:“结果处理”。     

公众科学在欧美生态环境研究和管理中的应用

近十年来以大量公众参与科学研究活动为特征的公众科学在生态环境研究和管理中得到了快速发展,根据公众和科学家之间的合作程度不同出现了以贡献型、协作型和共创型为主的应用模式,并在生物多样性调查、环境质量监测、生态环境管理中表现出了极大的潜在价值。通过对欧美公众科学在生态环境研究和管理中的典型案例进行介绍,分析了其概念内涵,概括了其项目的组成结构和应用模式,指出了面临的挑战和发展趋势。结论如下:(1)传感器技术的进步、便携式智能设备和移动网络普及使得公众获取周边生态环境信息的能力日益增强,种类也日益多样。(2)公众科学项目的运用不仅能够扩大数据获取范围,也能加深公众对科学问题的认识和提高管理部门科学决策水平。(3)公众提供的数据种类,数据质量,以及公众激励机制,都是该模式持续和高质量运行时所要面临的挑战。(4)欧美一些"科研单位-公众机构-公民团体"等纷纷联合起来形成公众科学协会,同时政府部门已制定了公众科学发展计划和法规,来规范和促进公众科学项目的应用。(5)我国相关研究和管理部门应建立统一协作平台,进一步引导公众科学参与和提高协作效率。     

浅谈高中生物学的探究性实验(1)

科学探究是人们获得知识和认识世界的一种重要方法和过程 ,也是提高生物学教学质量的核心。所谓的科学探究 ,是指科学家研究自然界 ,并基于研究获得的证据提出各种理论的途径和方法 ,也是指学生用以获取知识、领悟各种科学思想观念、领悟科学家研究自然界的方法而参与的各种活动。因此 ,探究是学科学的中心环节。本文仅就高中生物学的实验分级、探究实验的活动程序等 ,谈谈自己的体会如下 :1　以探究为核心的实验分级以探究为核心对高中生物学的实验进行分级 ,有助于准确制定实验教学目标 ,有助于设计出最佳的实验方案 ,从而为取得理想的实…     

生物化学综合性与设计性实验实践探索

一般来说,在基础性验证性实验中包括传统的生物化学实验。对于这种实验,学生以实验指导书设计好的步骤为依据按部就班的完成即可,这种实验可以预知实验结果,能够预知实验中可能出现的问题,就一定程度而言,这种实验对学生想象力具有束缚作用。而综合性与设计性实验需要学生自己完成准备实验材料和配制试剂等等整个实验需要的东西。在学生眼里每一个环节具有全新性和挑战性。而且无法预料实验结果,学生必须分析总结实验中出现的现象和结果,因此说综合性和设计性实验有利于学生勇于创新和敢于挑战精神的培养。     

比较医学动物实验计算机辅助设计系统的研发

目的开发一款辅助研究者设计比较医学动物实验方案和学习实验设计的应用软件。方法根据实验动物应用的"科学、伦理、经济"原则筛选比较医学动物实验技术资料,运用关系数据库架构原理分析和组织入选数据,通过解析比较医学动物实验规律和特点设计程序框架和模块,采用C++语言、MFC库进行面向用户的程序设计。结果建立了程序相关资源库和模型选择、实验动物、环境条件、实验步骤、方案输出5个功能模块,并完成整个软件测试。结论研发成功比较医学动物实验计算机辅助设计系统,该系统能够基于微型计算机为用户提供有效、易用的动物实验辅助设计和自助学习功能。     

研究发现物种灭绝有连带作用

例1,[第(2)部分第31题]胰高血糖素对小白鼠和人具有相同的生理作用。为了验证“胰高血糖素具有升高血糖的生理作用”,请以小白鼠为实验对象设计实验步骤,预测和解释实验应出现的结果,并写出实验结论。(一)实验材料和用具:正常实验小白鼠2只,生理盐水,用生理盐水配制的适宜浓度的胰高血糖素溶液,班氏糖定性试剂,注射器,试管,烧杯等。(二)实验步骤:(实验提示:采用腹腔注射给药,给药剂量不作实验设计要求;给药1h后,用注射器在小鼠膀胱处穿刺取尿液。)(三)实验结果的预测、解释和结论:答案:(二)实验步骤:(1)确定一只鼠为实验鼠,腹腔注射胰高血糖…     

生物多样性数字图书馆系统的架构和实现

生物多样性研究工作急切需要一个建立在多源数据基础上的数字图书馆。基于虚拟用户社区的生物多样性数字图书馆除了在数据类型、存储需求、共享方式等方面具有一般数字图书馆的特点之外, 在数据挖掘和应用方面也有自己的一些特点。本文在对国内外数字图书馆调研和与生物多样性遗产图书馆(Biodiversity Heritage Library)及互联网档案(Internet Archive)项目的合作的基础上, 总结了各类数字图书馆中的数据类型, 对构建生物多样性数字图书馆相关的数据标准——Dublin Core和TaxonX作了简单介绍。然后设计了具有数据汇总、数据整理、转换和翻译以及数据对外服务三个模块的系统框架,提出了生物多样性数字图书馆的系统架构和功能,展示了已经实现的部分系统运行效果, 最后对今后在版权、全文识别、海量和扩展等方面的问题进行了讨论。     

“中国力学虚拟人”研究及应用

该课题利用"中国可视化人"项目研究成果和志愿者的相关数据,建立了人体全身和部分细分部位的骨肌系统生物力学仿真模型。模型可以按真实对象进行改造,并可植入人工关节等植入物。在所建实验平台中,通过运动捕捉系统测得的或人为设计的运动数据,模型可以仿真人体各种行为运动,进行动力学分析,计算关节力、关节力矩和肌肉力。成果集成在所开发的软件CMVHuman1.0中,完成软件注册登记,并建立了产业化服务体系。成果已在临床医学和植入物设计中获得广泛应用,并扩大到体育科学、人体工程学、航空、航天和虚拟士兵等领域。     

“探究种子萌发的外界条件”一节的教学活动设计

1　对象　初二年级学生。2　教学目的1)通过学生亲自设计实验 ,探究种子萌发需要哪些外界条件 ,使学生学会设计对照实验 ,懂得控制实验条件 ,检验单一因子对种子萌发的影响 ,从而进行科学方法的训练 ,培养学生的科学素质。2 )通过学生参与实验设计 ,并对实验结果加以观察分析 ,培养学生的实践能力 ,发展学生的创造力 ,提高学生分析问题的能力。3)通过分组讨论实验方案 ,共享实验成果 ,对学生进行协作精神的教育。3　活动时间、地点、活动方式上课时间 ,实验室 ,集体讨论的方式。4　教学活动过程4 .1　引导学生提出假设　请生物学课外小组的…     

Process-oriented ecological modeling approach and scientific workflow system

A scientific workflow system is designed specifically to organize, manage and execute a series of research steps, or a workflow, in a given runtime environment. The vision for scientific workflow systems is that the scientists around the world can collaborate on designing global-scaled experiments, sharing the data sets, experimental processes, and results on an easy-to-use platform. Each scientist can create and execute their own workflows and view results in real-time, and then subsequently share and reuse workflows among other scientists. Two case studies, using the Kepler system and BioVeL, are introduced in this paper. Ecological niche modeling process, which is a specialized form of scientific workflow system included in both Kepler system and BioVeL, was used to describe and discuss the features, developmental trends, and problems of scientific workflows.     

Development of a cloud-based platform for reproducible science: A case study of an IUCN Red List of Ecosystems Assessment

One of the challenges of computational-centric research is to make the research undertaken reproducible in a form that others can repeat and re-use with minimal effort. In addition to the data and tools necessary to re-run analyses, execution environments play crucial roles because of the dependencies of the operating system and software version used. However, some of the challenges of reproducible science can be addressed using appropriate computational tools and cloud computing to provide an execution environment.Here, we demonstrate the use of a Kepler scientific workflow for reproducible science that is sharable, reusable, and re-executable. These workflows reduce barriers to sharing and will save researchers time when undertaking similar research in the future.To provide infrastructure that enables reproducible science, we have developed cloud-based Collaborative Environment for Ecosystem Science Research and Analysis (CoESRA) infrastructure to build, execute and share sophisticated computation-centric research. The CoESRA provides users with a storage and computational platform that is accessible from a web-browser in the form of a virtual desktop. Any registered user can access the virtual desktop to build, execute and share the Kepler workflows. This approach will enable computational scientists to share complete workflows in a pre-configured environment so that others can reproduce the computational research with minimal effort.As a case study, we developed and shared a complete IUCN Red List of Ecosystems Assessment workflow that reproduces the assessments undertaken by Burns et al. (2015) on Mountain Ash forests in the Central Highlands of Victoria, Australia. This workflow provides an opportunity for other researchers and stakeholders to run this assessment with minimal supervision. The workflow also enables researchers to re-evaluate the assessment when additional data becomes available. The assessment can be run in a CoESRA virtual desktop by opening a workflow in a Kepler user interface and pressing a “start” button. The workflow is pre-configured with all the open access datasets and writes results to a pre-configured folder.     

Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis

Environmental sensor networks are now commonly being deployed within environmental observatories and as components of smaller-scale ecological and environmental experiments. Effectively using data from these sensor networks presents technical challenges that are difficult for scientists to overcome, severely limiting the adoption of automated sensing technologies in environmental science. The Realtime Environment for Analytical Processing (REAP) is an NSF-funded project to address the technical challenges related to accessing and using heterogeneous sensor data from within the Kepler scientific workflow system. Using distinct use cases in terrestrial ecology and oceanography as motivating examples, we describe workflows and extensions to Kepler to stream and analyze data from observatory networks and archives. We focus on the use of two newly integrated data sources in Kepler: DataTurbine and OPeNDAP. Integrated access to both near real-time data streams and data archives from within Kepler facilitates both simple data exploration and sophisticated analysis and modeling with these data sources.     

Analysing scientific workflows with Computational Tree Logic

Motivated by the widespread use of workflow systems in e-Science applications, this article introduces a formal analysis framework for the verification and profiling of the control flow aspects of scientific workflows. The framework relies on process algebras that characterise each workflow component with a process behaviour, which is then used to build a CTL state model that can be reasoned about. We demonstrate the benefits of the approach by modelling the control flow behaviour of the Discovery Net system, one of the earliest workflow-based e-Science systems, and present how some key properties of workflows and individual service utilisation can be queried at design time. Our approach is generic and can be applied easily to modelling workflows developed in any other system. It also provides a formal basis for the comparison of control aspects of e-Science workflow systems and a design method for future systems.     

Response Surface Modelling for Performance Analysis of Scientific Workflow Application in Cloud

Scientific workflow applications are used by scientists to carry out research in various domains such as Physics, Chemistry, Astronomy etc. These applications require huge computational resources and currently cloud platform is used for efficiently running these applications. To improve the makespan and cost in workflow execution in cloud platform it requires to identify proper number of Virtual Machines (VM) and choose proper VM type. As cloud platform is dynamic, the available resources and the type of the resources are the two important factors on the cost and makespan of workflow execution. The primary objective of this work is to analyze the relationship among the cloud configuration parameters (Number of VM, Type of VM, VM configurations) for executing scientific workflow applications in cloud platform. In this work, to accurately analyze the influence of cloud platform resource configuration and scheduling polices a new predictive modelling using Box–Behnken design which is one of the modelling technique of Response Surface Methodology (RSM). It is used to build quadratic mathematical models that can be used to analyze relationships among input and output variables. Workflow cost and makespan models were built for real world scientific workflows using ANOVA and it was observed that the models fit well and can be useful in analyzing the performance of scientific workflow applications in cloud

     

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

Background

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts.

Results

In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.

Conclusions

Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis. The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.     

Taverna: a tool for the composition and enactment of bioinformatics workflows

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.