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Keywords: Bioinformatics
(Complete Item Description)
- Abstract: This course provides a broad introduction to machine learning and statistical pattern recognition. Topics include: supervised learning (generative/discriminative learning, parametric/non-parametric learning, neural networks, support vector machines); unsupervised learning (clustering, dimensionality reduction, kernel methods); learning theory (bias/variance tradeoffs; VC theory; large margins); reinforcement learning and adaptive control.
The course will also discuss recent applications of machine learning, such as to robotic control, data mining, autonomous navigation, bioinformatics, speech recognition, and text and web data processing.
(Complete Item Description)
- Abstract: This interdisciplinary course provides a hands-on approach to students in the topics of bioinformatics and proteomics. Lectures and labs cover sequence analysis, microarray expression analysis, Bayesian methods, control theory, scale-free networks, and biotechnology applications. Designed for those with a computational and/or engineering background, it will include current real-world examples, actual implementations, and engineering design issues. Where applicable, engineering issues from signal processing, network theory, machine learning, robotics and other domains will be expounded upon.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
(Complete Item Description)
- Abstract: This undergraduate activity introduces students to bioinformatics. During the guided activity students will access the National Center for Biotechnology Information's (NCBI) genetic sequence database to obtain and study DNA sequence entries relating to the chicken ovalbumin mRNA and genomic sequences.
(Complete Item Description)
- Abstract: This educational journal article addresses the implementation of bioinformatics in the classroom. The author explains how bioinformatics could play a key role for science students pursuing higher education, foster inquiry learning of content that has often been taught in a dry manner, provide the thread that ties classes together, improve biology teaching, enhance the learning of biotech issues and ethics, expose students to real-world science, and significantly help to reform biology teaching and improve learning. The article includes links to bioinformatics resources, information about how to get involved in bioinformatics, and a glossary of terms.
(Complete Item Description)
- Abstract: This project is designed to give the student experience using the bioinformatics tools that have been taught in previous modules in an independent project. The student will use the project outline to develop a bioinformatics problem or question according to their interests, and determine the appropriate tools to answer the question.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: This is an introduction to the bioinformatics website provided by the National Center for Biotechnology Information (NCBI). It includes an overview of the basic mission of NCBI and an introduction to the most commonly used biological databases available on the website and the tools for viewing and analyzing the data.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: The objective of this subject is to teach the design of contemporary information systems for biological and medical data. These data are growing at a prodigious rate, and new information systems are required. This subject will cover examples from biology and medicine to illustrate complete life cycle information systems, beginning with data acquisition, following to data storage and finally to retrieval and analysis. Design of appropriate databases, client-server strategies, data interchange protocols, and computational modeling architectures will be covered. Students are expected to have some familiarity with scientific application software and a basic understanding of at least one contemporary programming language (C, C++, Java, Lisp, Perl, Python, etc.). A major term project is required of all students. Reading is assigned from the contemporary literature, and there is occasional homework.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
(Complete Item Description)
- Abstract: The objective of this subject is to teach the design of contemporary information systems for biological and medical data. These data are growing at a prodigious rate, and new information systems are required. This subject will cover examples from biology and medicine to illustrate complete life cycle information systems, beginning with data acquisition, following to data storage and finally to retrieval and analysis. Design of appropriate databases, client-server strategies, data interchange protocols, and computational modeling architectures will be covered. Students are expected to have some familiarity with scientific application software and a basic understanding of at least one contemporary programming language (C, C++, Java, Lisp, Perl, Python, etc.). A major term project is required of all students. Reading is assigned from the contemporary literature, and there is occasional homework.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
(Complete Item Description)
- Abstract: Computer laboratory modules for the Introduction to Bioinformatics course. This course is designed for the beginning graduate student or advanced undergraduate in the biosciences. The goal is to introduce the student to various biologically relevant databases, methods to effectively search the databases, and an overall view of the various aspects of computational biology.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: This interactive tutorial is designed as a quick introduction to the BLAST family of sequence analysis programs. These slides show a progression of steps in accessing and using BLAST, beginning at the home page for the National Center for Biotechnology Information (NCBI) and ending at PubMed, a tool for searching scientific literature. In this series, a nucleotide sequence is submitted and compared, using blastn, to GenBank, a comprehensive database of biological sequences.
(Complete Item Description)
- Abstract: This site features an undergraduate Computational Biology course as part of the Red Layer Microbial Observatory (RLMO) Project's Original Waksman/NSF supported courses and workshops. The course is offered as part of RLMO's education and outreach in order to better prepare students in the widely-applicable field of computational biology. Unit outlines, the syllabus, the project, and presentations and manuscripts about this curriculum can all be downloaded on site. Units include using NCBI, using BW/Datasets, multiple sequence alignment, phylogenetic tree-building, and protein structure. The website also features an image and data (3D viewer required) of the structure of ribosomal proteins and 16S rRNA from T. thermophilus.
(Complete Item Description)
- Abstract: This information database provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, and are believed to be the ancient ancestors of chloroplast. Maintained by the Kazusa DNA Research Institute, Cyanobase contains information and sequences for Synechocystis, Anabaena, Thermosynechococcus elongatus, Gloeobacter violaceus, Prochlorococcus marinus, Synechococcus, Chlorobium tepidum, and Rhodopseudomonas palustris. It also includes links to CyanoMutants, a database depository of published and unpublished functional and genetic data on Synechocystis 6803 mutants with known mutations, and CyanoGenes.
(Complete Item Description)
- Abstract: This module explores the Synergix drug design resources web site. The relationship between drug discovery and bioinformatics is discussed. Several examples of bioinformatics methods used in the design of pharmaceutical are examined.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: This course provides an interdisciplinary introduction to the technological advances in biomedical informatics and their applications at the intersection of computer science and biomedical research.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
(Complete Item Description)
- Abstract: This module is an introduction to performing searches of the NCBI databases using Entrez, the NCBI web-based search and retrieval tool for integrated search results from multiple databases.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: This module describes the many proteomics tools available from the ExPASy website. Tools are introduced for protein identification and characterization from amino acid composition, fingerprint mass spectroscopy and other mass spectroscopy techniques. A
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: This is part II in a two-part series describing the many proteomics tools available from the ExPASy website. This module introduces tools for protein topology prediction, Primary structure analysis, Secondary structure prediction and tertiary structure
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
Connexions
(Complete Item Description)
- Abstract: Laboratory uses yeast as an experimental system to study fundamental problems in understanding cell cycle and chromosome segregation. Experimental work combines genetic approaches with the tools of molecular and cell biology to identify and characterize novel genes that act on these processes. Instruction and practice in written and oral communication provided.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
(Complete Item Description)
- Abstract: Introduction to computational biology including the fundamentals of protein and nucleic acid sequence analysis, phylogenetic analysis, motif finding, hidden Markov models, and 3D structure prediction and modeling. An overview of emerging fields including expression profiling, quantitative image analysis and the modeling of cellular signal transduction networks are also included. Subject designed for advanced undergraduates and graduate students with strong backgrounds in either molecular biology or computer science but not necessarily both. Two self-study tracks are offered, introducing either basic statistical methods and programming (to biologists) or the fundamentals of molecular biology (to computer scientists). Lectures combine both perspectives to illustrate how computation is having a significant impact on modern biology. Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology.
- Subject:
Science and Technology
- Grade Level:
Post-secondary
- Collection:
MIT OpenCourseWare
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