E-Learning as a new tool in bioinformatics teaching

In recent years, virtual learning is growing rapidly. Universities, colleges, and secondary schools are now delivering training and education over the internet. Beside this, resources available over the WWW are huge and understanding the various techniques employed in the field of Bioinformatics is increasingly complex for students during implementation. Here, we discuss its importance in developing and delivering an educational system in Bioinformatics based on e-learning environment.     

GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses

The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or 'in the cloud' using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/.     

本科生助教模式在微生物学实验教学中的探索与实践

微生物学是水产养殖专业的一门重要的专业课,其实验教学则是将理论知识转化为实践能力的重要途径,在专业人才培养中占据重要地位。由于微生物学实验具有操作过程烦琐、耗时较长等特点,在有限的课时内,学生无法经历每一个实验步骤,系统完成全部实验过程,教学效果往往不尽如人意。本文将本科生助教模式应用于微生物学实验教学中,让助教利用碎片化的时间进入实验室,参与实验设计、试剂和培养基配制、微生物分离和纯化等工作,掌握较扎实的实验技能,然后回到课堂,充当师生沟通的桥梁,协助教师指导学生实验。助教的学习兴趣和综合素质得以提高,学生在实验中的错误得到及时纠正,教学效果也得到提升。     

PBL双语教学在八年制本科神经病学教学初探

八年制临床医学神经病学专业本科教育是一个互动性较强的教学过程.采取PBL结合双语教学的授课模式,能够较好地促进学生自主学习、活跃临床思维,教学效果理想.PBL结合双语教学为培养具有创新性和国际视野的高层次、高水平临床医学尖端人才奠定了厚实的基础.     

A review of bioinformatics degrees in Australia

Bioinformatics has been a hot topic in Australia's biotechnology circles for the past five years. As with biotechnology in the 1990s, there has been a sudden increase in the number of Bioinformatics undergraduate degrees. For students in the 2005 intake there are six undergraduate Bioinformatics degrees to choose from and another five Bioinformatics streams within a Bachelor of Science degree. The courses vary from three to four years of full-time study. This report aims at dissecting each of these degrees to determine where the differences lie, to give the prospective students an idea as to which degree suits their career goals and to give an overview of the pedagogy of Australian bioinformatics education.     

案例教学法在护理本科专业组织学与胚胎学教学中的实施与体会

组织学与胚胎学为护理本科专业学生必修课.在教学过程中采取＂学生为主体、教师为主导＂的案例教学法,激发学生的主观能动性,注重学生创新能力培养.在案例教学过程中,也发现一些问题：学生素质不一、学习目标不明确以及教师教育理念滞后等.因此,在护理本科专业组织学与胚胎学实施案例教学过程中,引导学生确立学习目标,积极思考,注重团队合作,全面调动学生学习的积极性和主动性.教师在更新教学观念的同时,提倡奉献精神,注重自身素质的培养和提高.     

《生物信息学》课程教学模式探讨

在教学实践的基础上,结合生物信息学课程的学科特点,以及现代教育技术,就开设生物信息学课程的必要性及构建最合适的复合型教育模式展开了初步的探讨,为我国生物信息学课程的教学实施提供指导。随着时代的不断进步和发展,生物信息学的内涵也在不断扩大,包括生物信息学所涉及到的计算机基础知识、生物学基础知识、生物信息学研究领域、生物信息学应用领域等等。在生物信息学的教学实施过程中,将多个基础学科交叉融合是必备的,这不仅有助于增强学生对生物信息学科的了解,也对于学生在后续的生物信息学研究中起到了基石的作用。因此,如何将这些涉及范围广、涉及内容深的生物信息学基础课程恰当的传授给学生是教师们最需要考虑的问题,从而形成一套独特的教学体系,使生物信息学的教学工作更顺利,完整的进行下去。     

硕士研究生参与本科生组织学与胚胎学实验课教学的体会

硕士研究生通过参与本科生组织学与胚胎学实验课教学,可加深对本专业知识的理解,建立更合理的知识结构,完善自身的思维体系,提高综合能力,从中发现自身不足之处并积极弥补。硕士研究生参与本科生教学具有独特的优势,对提升其综合素质有所助益。     

应用型本科院校食品微生物学双语教学的探讨

双语教学有利于促进教育与国际接轨,对于促进学科与学术前沿融合具有重要的意义,作为我国高等教育的新生力量——应用型本科院校,有必要实施食品微生物学双语教学。分析了应用型本科院校食品微生物学实施双语教学的必要性,并对其可行性提出了自己的见解。     

强化生物信息学实践教学的探索与成果

生物信息学是一门数学、统计、计算机与生物医学交叉结合的新兴学科。文章依据对生物技术和生物科学专业本科生开展新模式下的《生物信息学》教学实践,对教学模式进行全面深入改革与创新,实现理论教学、实践教学和网络教学的完美融合,创建了新世纪科学性教学体系,全面提高教学质量和水平,培养综合型人才。     

生物信息学研究新基因LRP15

为了利用生物信息学探索网上克隆基因与预测基因功能的新方法,首先用一段1.8kbDNA片段的人类EST数据库中进行电子杂交并对相互重叠的EST片段组装,通过引物设计进行cDNA末端快速扩增,以高通量基因组序列（HTGS）数据库及SAGE库为基础,进行染色体定位及组织表达分析。通过DAS及RPS－BLAST程序预测其蛋白质结构及功能。结果显示,LRP15 cDNA全长1718bp,含一个780bp的开放读码框架,编码259个氨工酸,该基因定位于染色体3p24,在多种组织中表达。其编码蛋白含有N端富含亮氨酸重复序列及潜在的穿膜序列。研究表明,生物信息学是克隆与预测基因功能的有效方法;LRP15基因可能是一个参与细胞发育调控的新基因。     

生物化学与分子生物学本研教学一体化探索与实践

生物化学(Biochemistry)和分子生物学(Molecular Biology)课程是生命科学领域人才培养的基石。本研究以这些课程为桥梁,从知识框架重构、教学案例建设、教学资源共享、教学手段更新、立德树人格局的建立等方面入手,以学科特色科研成果案例和在线教学平台为支撑,通过课程教学实践,探索了以科研育人为导向,以课程建设为根基,以交流合作为推动力的本研一体化课程改革模式,搭建了“交流、实践、开放、信息化”的共享空间,实现了本、研教学以汲取知识为动力的自由、自主融合,使学生培养成效得到了提升。     

合成生物学底盘微生物细胞的应用及其生物安全在创新型本科生培养中的实践

本科生创新能力培养是"双一流"建设人才培养的重要组成部分。合成生物学是一门新兴多学科交叉领域,被誉为可改变世界的十大新技术领域之一。构建高版本底盘微生物细胞和利用底盘细胞人工合成细胞工厂是合成生物学的重要组成部分。以实现创新型本科生为培养目标,我们将合成生物学底盘微生物细胞技术融入人才培养环节,通过组织学生参加国际遗传工程机器设计竞赛、主持大学生创新创业训练项目以及完成本科生毕业设计课题等多元化途径,提高学生理论联系实际及创新实践能力。同时,由于底盘微生物细胞是基因组经过精简、优化或其基因通路被改变的细胞,其应用存在一定的生物安全风险。我们通过将安全教育纳入培养大纲和教学计划、出版实验室安全与操作规范专业教材、开发虚拟仿真实验项目、建立实验室准入制度和信息化管理体系,以及针对底盘微生物细胞从购买、管理、规范使用和废弃物处理等进行生物安全教育等系列举措,规范底盘微生物细胞应用的生物安全。这些实践为培养创新型本科生提供了一个强有力的途径和有效保障,也为合成生物学的发展提供了支持,并有助于培养新的生力军。     

Understanding the yeast proteome: a bioinformatics perspective

Rapid development of genomic and proteomic methodologies has provided a wealth of data for deciphering the biomolecular circuitry of a living cell. The main areas of computational research of proteomes outlined in this review are: understanding the system, its features and parameters to help plan the experiments; data integration, to help produce more reliable data sets; visualization and other forms of data representation to simplify interpretation; modeling of the functional regulation; and systems biology. With false-positive rates reaching 50% even in the more reliable data sets, handling the experimental error remains one of the most challenging tasks. Integrative approaches, incorporating results of various genome- and proteome-wide experiments, allow for minimizing the error and bring with them significant predictive power.     

Epitopemap: a web application for integrated whole proteome epitope prediction

Background

Predictions of MHC binding affinity are commonly used in immunoinformatics for T cell epitope prediction. There are multiple available methods, some of which provide web access. However there is currently no convenient way to access the results from multiple methods at the same time or to execute predictions for an entire proteome at once.

Results

We designed a web application that allows integration of multiple epitope prediction methods for any number of proteins in a genome. The tool is a front-end for various freely available methods. Features include visualisation of results from multiple predictors within proteins in one plot, genome-wide analysis and estimates of epitope conservation.

Conclusions

We present a self contained web application, Epitopemap, for calculating and viewing epitope predictions with multiple methods. The tool is easy to use and will assist in computational screening of viral or bacterial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0659-0) contains supplementary material, which is available to authorized users.     

A survey of the availability of primary bioinformatics web resources

The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources （such as software tools and databases）. The majority （95%） of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache （or Apache-related products）. Of the overall 1,130 Uniform Resource Locators （URLs） examined, 91% were highly available （more than 90% of the time）, while only 4% showed low accessibility （less than 50% of the time） during the survey. Furthermore, the most common URL failure modes are presented and analyzed.