INTRODUCTION TO BIOINFORMATICS

生物信息学导论

• 批准号: 7956284
• 负责人: Shalun Lewis
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956284
• 关键词: Absenteeism at work; Accountability; Admission activity; Age; Algorithms; Amendment; American; Arabidopsis; Area; Arts; Award; Bacillus subtilis; Base Sequence; Behavior; Bioinformatics; Biology; Biomedical Research; Cataloging; Catalogs; Cellular Phone; Chemistry; Civil Rights; Collection; Color; Communities; Community Services; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Computers; Culicidae; DNA; Data; Databases; Dedications; Devices; Disabled Persons; Discipline; Drops; Educational process of instructing; Electronics; Emergency Situation; Employment; Escherichia coli; Ethics; Evaluation; Exercise; Faculty; Foundations; Freedom; Funding; Gene Proteins; Genes; Genetic; Genome; Genomics; Gifts; Goals; Grant; Hand; Hand functions; High Performance Computing; Historically Black Colleges and Universities; Holidays; Human; Human Genome; Human Rights; Institution; Instruction; Internet; Internships; Isoenzymes; Knowledge; Laboratories; Laws; Learning; Legal patent; Manufactured football; Mathematics; Medicine; Methods; Minority; Molecular; Molecular Biology; Morals; Mus; National origin; Oklahoma; Operating System; Pattern; Personal Digital Assistant; Persons; Phylogenetic Analysis; Physicians; Plagiarism; Plants; Policies; Polymerase Chain Reaction; Population; Private Sector; Procedures; Pythons; Race; Rattus; Regulation; Religion; Reporting; Research; Research Personnel; Resources; Rewards; Rice; Schedule; Scholarship; Schools; Science; Scientist; Sequence Alignment; Sequence Analysis; Services; Social Responsibility; Solid; Solutions; Source; Structure; Students; Suspension substance; Suspensions; System; Technology; Testing; Text; Time; Underserved Population; United States National Institutes of Health; Universities; Veterans; Vision; Withdrawal; Work; Writing; aldehyde dehydrogenases; authority; base; career; computer science; court; disability; distraction; experience; falls; handicapping condition; innovation; instructor; interest; journal article; lectures; mathematical model; meetings; member; microorganism; movie; probation; programs; rat genome; sex; statistics; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. LANGSTON UNIVERSITY SCHOOL OF ARTS AND SCIENCES DEPARTMENT OF BIOLOGY INTRODUCTION TO BIOINFORMATICS BI4133 FALL SEMESTER, 2007 FACULTY Dr. Sharon Lewis - 307 Hamilton Hall - [phone] [e-mail] OFFICE HOURS: MW from 10:00-3:00 p.m. OFFICE HOURS: Friday from 10:00-12:00 p.m. Dr. George Acquaah 404 Research Building - [phone] [e-mail] OFFICE HOURS: MWF from 10:00-11:00 a.m. Dr. Kanyand Matand  235 Research Building - [phone] [e-mail] OFFICE HOURS: MWF 10-1:00 p.m. Mr. Theophilus Depona- 219 Hamilton Hall  [phone] [e-mail] OFFICE HOURS: MWF 2-5 p.m. OFFICE HOURS: T Th 8-10 a.m. Organization Lecture Laboratory Days Tuesday Thursday Time 1-2:15 1-2:15 Room Research Bldg, rm 405 HamH 316A REQUIRED TEXT and MATERIALS Journal articles will be assigned for this class. CATALOG DESCRIPTION Bioinformatics is a collection of methods used for analyzing molecular biology data with a computer. A team of Langston University faculty from various disciplines (chemistry, biology, mathematics, computer science, and research) will teach this course with the goal of cultivating research-oriented minority students for careers in bioinformatics. Interested students can compete for summer internships at PSC. RATIONALE Bioinformatics is an area of research developing as a result of the Human Genome Initiative and the advent of the World Wide Web, shortly thereafter. Once patented technology such as the polymerase chain reaction and the DNA sequencer were developed, molecular biologist began sequencing entire genomes from human, rat, and mouse to plants, such as rice and Arabidopsis, to microorganisms such as E. coli and Bacillus subtilis. The scientist quickly realized that someone needed to provide tools for collection, storage, and analysis of this exponentially growing amount of nucleotide sequences. Computer scientist were needed to write scripts to allow for the assembly of entire genomes and comparison of genes within the genomes and between genomes (rat with human with mosquitos. Computer scientist quickly realized that mathematicians were needed for the intricate details of statistics, algorithms, and matrices. Bioinformatics is a multi-disciplinary field that is constantly evolving to meet the demands of the post-genomic area, if there is one, aiming for the diminishless field of personalized medicine. COURSE OBJECTIVES The student should: 1. Define Bioinformatics and understand how this discipline evolved. 2. Complete the Unix Operating System Hands- On Exercise. 3. Retrieve Sequences from Databases and Complete Hands- On Exercise. 4. Complete the Database Searching and Alignment Hands-On Exercise. 5. Complete the Multiple Sequence Alignment Hands-On Exercise. 6. Complete the Pattern Identification and Matching Hands-On Exercise. 7. Complete the Python Exercises. 8. Complete the Phylogenetic Analysis Hands-On Exercises. 9. Complete the Finding Features in Groups of Sequences Hands-On Exercises. METHOD OF INSTRUCTION This class will be taught by a team of faculty who have experience in their fields of research. The faculty will use hands-on exercises, powerpoint presentations, and journal articles when presenting their information. COURSE REQUIREMENTS Each student should: 1. Attend all classes, punctually. 2. Complete all hands-on exercises. Take all exams or quizzes. 3. Complete your project. 4. Present your project. METHOD OF EVALUATION- Points for course requirements Each faculty member will assess the students as the subject matter lends itself. Minimum Grade Requirement: A = 90%; B = 80%; C = 70%; D = 60%; F = below 59% 3. Class Attendance It is imperative that students attend all lectures and labs. Material covered during each session is critical and is prerequisite to subsequent material. Material missed in one lecture can seriously hinder the student(s ability to comprehend related material. An attendance sheet will circulate at the beginning of class. Classes will be held daily. If no laboratory assignments are scheduled, then classes will be held in the recitation room. Six (6) absentees can result in an administrative withdrawal. The Office of Academic Affairs will give excused absences in the following two areas ONLY: Participation in University Functions (Who is on the Football Team?), and illness as documented with an official statement from the attending physician. Academic Integrity- NO CHEATING The following will apply to cases of academic dishonesty. The instructor ordinarily has final authority over the grades given to students or the lowering of grades because of cheating or plagiarism. If it is established by clear and convincing evidence that cheating or plagiarism has occurred, a) The instructor will take appropriate academic disciplinary action which may include the awarding of an "F" on the particular assignment or in the course. b) The instructor will make a report of the incident and of action taken, if any, to the departmental chair, the Vice President for Academic Affairs, Vice President for Student Affairs, and the student. c) The Student Disciplinary Committee may review the incident and impose conduct discipline, including conduct probation and suspension. d) The student may, if he/she so desires, discuss the matter with the Student Disciplinary Committee and/or the Student Judicial Court. Policy on Electronic Devices in the Classroom-NO CELLPHONES RINGING DURING TEST All electronic devices (e.g., cell phones, pagers, palm pilots, beeper watches) are considered unnecessary distractions and are to be turned off and (with the exception of watches) concealed during class. Thus, interacting with these devices during class will not be tolerated. Instructors may make exceptions for instructional purposes. A student who anticipates an emergency and expects to be contacted in class by an outside source must go directly through the emergency dispatch system identified on each of the respective campuses. The emergency dispatcher will take the message and deliver it to the instructor. A student who fails to comply with this policy will be initially dismissed from the class and (per the Instructor's discretion) may be counted absent. Points may be deducted for work missed during that time. A student who violates this policy a second time will be dropped from the course for disruptive behavior. A student whose electronic device is activated during an exam will be dismissed from the class and denied the opportunity to complete or take that exam. An Instructor may elect not to grade that exam. Langston University: Vision Statement Langston University, a land grant Historically Black institution of higher learning, will continue its rich tradition of developing leaders from a diverse, multi-cultural student body through excellent teaching, research, community service and public and private sector partnerships. As Langston University moves from Excellence to Greatness, it will be recognized for providing solutions to problems facing underserved populations in Oklahoma, the nation, and the world. Langston University: Core Values 1. Strong work ethic and dedication: We are united in our dedication to working as hard and as long as necessary in order to realize our vision of developing creative solutions to the problems facing undeserved populations in Oklahoma, the nation and the world. 2. Passion for learning: Our zeal for knowledge, our quest to understand "why" and our desire to develop innovative answers, create a vibrant academic community. 3. Courage to have exemplary character: We are building a community in which high ethical and moral standards are maintained and valued by our faculty, staff, and students. 4. Excellence: We value, treasure and reward excellence in scholarship, teaching, and community service. 5. Scholarly innovation and a commitment to scholarship: We are a community of pragmatic intellectuals, using our knowledge to better our state, nation and the world. 6. Appreciation of difference: We believe firmly that everyone must be respected and that there is always more that one way to consider any issue. We value diversity of opinions, ideas, cultures, and perspectives. 7. Fiscal accountability: We believe that solid fiscal management is the foundation upon which a great university is built. 8. Social responsibility: We believe that knowledge is a gift which must be used to create a better world. 9. Commitment to fundamental human rights: Above all, we value the right of every human being to enjoy freedom, respect, and the opportunity to realize his or her potential. AFFIRMATIVE ACTION Langston University, in compliance with Title VI and VII of the Civil Rights Acts of 1964, Executive Order 11246 as amended, Title IX of the Educational Amendments of 1972, Americans with Disabilities Act of 1990, and other federal laws and regulations, does not discriminate on the basis of race, color, national origin, sex, age, religion, handicap, or status as a veteran in any of its policies, practices, or procedures. This includes, but is not limited to, admissions, employment, financial aid, and educational services. ADA STATEMENT Langston University fully subscribes to all required standards of The Americans with Disabilities Act of 1990 (ADA). Persons in need of assistance should contact The ADA Compliance Officer in the Office of Student Affairs, Room 119, Page Hall, [phone]. This should be reported at some point before, during, or immediately after the first scheduled class period so accommodations can be provided for the student to be successful in that class. SCHEDULE: WEEK DATE MATERIAL COVERED 1 8/20 21-Aug Introduction to Bioinformatics and Introduction of Faculty-Dr. Lewis 22-Aug 23-Aug DOE movie and Installing Programs on Computers-Dr. Lewis 24-Aug 2 8/27 28-Aug DNA, Genes, Proteins Biology Overview-Dr. Acquaah 29-Aug 30-Aug DNA, Genes, Proteins Biology Overview-Dr. Acquaah 31-Aug 3 9/3 Labor Day Holiday 4-Sep Genomes-Dr. Lewis 5-Sep 6-Sep Genomes-Dr. Matand/ Hands-On Exercises-Mr. Depona 7-Sep 4 9/10 11-Sep New Sequence Analysis-Dr. Lewis, Dr. Bucki 12-Sep 13-Sep New Sequence Analysis-Dr. Matand/ Hands-On Exercises-Mr. Depona 14-Sep 5 9/17 18-Sep Pairwise Alignment and Sequence Database Searches: Algorithm-Dr. Hugh Nicholas 19-Sep 20-Sep Evaluation-Dr. Jimmy Torres/ Hands-On Exercises-Mr. Depona 21-Sep 6 9/24 25-Sep Database_Search_Significance-Dr. Lewis, Dr. Bucki 26-Sep 27-Sep Database_Search_Significance-Dr. Matand/ Hands-On Exercises-Mr. Depona 28-Sep 7 10/1 2-Oct Database_Search-Matrices-Dr. Matand 3-Oct 4-Oct Applied Database Searching-Dr. Lewis, Hands-On Exercises-Mr. Depona 5-Oct Homecoming Break 8 10/8 Homecoming Break 9-Oct Mutiple Sequence Alignment-Dr. Hugh Nicholas-PSC 10-Oct Midterm Exam Period 11-Oct Mutiple Sequence Alignment-Examples-Dr. Hugh Nicholas-PSC 12-Oct 9 10/15 16-Oct Multiple Sequence Alignment Hands-on-Alex Ropelewski 17-Oct 18-Oct Introduction to Mathematical Methods- Mr. Depona 19-Oct 10 10/22 23-Oct Introduction to Mathematical Models in Computational Biology and Bioinformatics-Mr. Depona, Hands-On Exercises-Mr. Depona 24-Oct 25-Oct Hands-On Exercises-Mr. Depona 26-Oct 11 10/29 30-Oct Aldehyde Dehydrogenase Motifs, Bioinformatics, Structure, Function and Genetics-Dr. Acquaah 31-Oct 1-Nov Hands-On Exercises-Mr. Depona 2-Nov 12 11/5 6-Nov Analysis of Isozymes-Dr. Acquaah 7-Nov 8-Nov Your Project 9-Nov 13 11/12 13-Nov Your Project 14-Nov 15-Nov Your Project 16-Nov 14 11/19 20-Nov Your Project 21-Nov Last Day to Drop a class and receive a

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 兰斯顿大学艺术与科学系生物学系生物信息学介绍BI4133秋季学期，2007年教职员工Sharon Lewis博士 - 307 Hamilton Hall-[phone] [e-mail] Office.edu办公时间：MW从10：00-3：00 P.M. MW起办公时间：星期五晚上10：00-12：00 George Aceakaah博士404研究大楼 - [phone] [e-mail]办公时间：MWF：10：00-11：00上午10：00-11：00，Kanyand Matand博士235研究大楼 - [phone] [e-mail] Office Hours：MWF 10-1：MWF 10-1：00-P.M. Theophilus Depona先生 - 219 Hamilton Hall（405）466-3557 [e-mail]办公时间：MWF下午2-5点办公时间：上午8-10上午，组织讲座实验室日，星期四星期四时间1-2：15 1-2：15室研究大厦，RM 405 HAMH 316A需要为此课程分配文本和材料期刊文章。目录描述生物信息学是用于使用计算机分析分子生物学数据的方法的集合。来自各个学科（化学，生物学，数学，计算机科学和研究）的兰斯顿大学教师团队将教授这门课程，目的是培养以研究为导向的少数族裔学生从事生物信息学的职业。有兴趣的学生可以在PSC竞争暑期实习。理性生物信息学是由于人类基因组倡议和万维网的出现而发展的研究领域。一旦开发了专利的技术（例如聚合酶链反应和DNA测序仪），分子生物学家就开始对整个基因组进行从人，大鼠和小鼠到植物的整个基因组，例如水稻和拟南芥，例如大肠杆菌和枯草菌等微生物。科学家很快意识到，有人需要提供用于收集，存储和分析的工具，以呈指数增长的核苷酸序列。需要编写脚本来编写计算机科学家，以允许整个基因组组装和基因组中的基因和基因组之间的比较（与人类与蚊子的大鼠。计算机科学家很快意识到，数学家需要数学家才能获得统计学，算法，算法和矩阵的复杂细节。因此，生物信息是一个多difipial的领域，不断地符合Is的要求，而不是与众多的领域相遇，而不是与统计学家相遇，并且需要与之相遇。一个人的目的是，学生应有的目标：1。动手练习7。完成Python练习。 9。完成一组序列动手练习的发现功能。教学方法这堂课将由在研究领域有经验的教师团队教授。在介绍信息时，教师将使用动手练习，PowerPoint演示文稿和期刊文章。课程要求每个学生应：1。准时参加所有课程。 2。完成所有动手练习。参加所有考试或测验。 3。完成您的项目。 4。介绍您的项目。课程要求的评估方法 - 每个教职员工都会在主题上评估学生。最低等级要求：A = 90％； B = 80％; C = 70％； d = 60％; F =低于59％3。上课的学生必须参加所有讲座和实验室。每次会议期间涵盖的材料至关重要，并且是随后材料的先决条件。一个讲座中错过的材料会严重阻碍学生（S理解相关材料的能力。出勤表将在上课开始时流通。每天举行课程。如果没有安排实验室的任务。如果安排了实验室任务，则课程将在朗诵室中举行。六（6）缺席会导致在行政上撤回的戒烟。在以下领域中，有两个领域的缺席。只有两次竞争的竞争方式：参与效果（该课程）（谁来参与）（谁来参与）？主教的官方声明。课程。 b）讲师将向部门主席，学术事务副总裁，学生事务副总裁和学生提交事件和行动（如果有的话）。 c）学生纪律委员会可以审查事件并施加行为纪律，包括行为缓刑和暂停。 d）如果学生如此渴望，则可以与学生纪律委员会和/或学生司法法院讨论此事。在测试期间，所有电子设备（例如，手机，打印机，棕榈飞行员，蜂鸣器手表）在课堂上响起的电子设备的政策被认为是不必要的分散注意力，并且要关闭，并且（除了手表外）隐藏了上课时。因此，在课堂上与这些设备的交互将无法忍受。教师可能会出于教学目的做出例外。预计紧急情况并希望在课堂上与外部来源联系的学生必须直接通过各自校园上确定的紧急调度系统。紧急调度员将获取消息并将其交付给教练。不遵守此政策的学生最初将被驳回班级，并且（根据教师的酌处权）可能会被计算在内。在此期间，可能会扣除积分的时间。第二次违反该政策的学生将从课程中删除颠覆性行为。在考试期间激活电子设备的学生将被解雇，并否认有机会完成或参加考试。讲师可以选择不给考试评分。兰斯顿大学（Langston University）：愿景宣言兰斯顿大学（Langston University）是一家土地赠款历史上的黑人高等教育机构，将继续其丰富的传统，即通过出色的教学，研究，社区服务以及公共和私营部门的伙伴关系，从多样化的多元文化学生团体发展领导者。随着兰斯顿大学（Langston University）从卓越到伟大的发展，它将因为俄克拉荷马州，国家和世界服务不足人群面临的问题提供解决方案而得到认可。兰斯顿大学：核心价值观1。强大的职业道德和奉献精神：我们团结一致地致力于努力和必要的努力，以实现我们对俄克拉荷马州，国家和世界不当的人口面临的问题的创造性解决方案的愿景。 2。学习的热情：我们对知识的热情，我们对了解“为什么”的追求以及我们建立创新答案，创造一个充满活力的学术界的愿望。 3。具有示例性的勇气：我们正在建立一个社区，在该社区中，我们的教职员工，教职员工和学生维持和评估高道德和道德标准。 4。卓越：我们在奖学金，教学和社区服务方面重视，宝藏和奖励卓越。 5。学术创新和对奖学金的承诺：我们是一个务实的知识分子社区，利用我们的知识来改善我们的国家，国家和世界。 6.差异的欣赏：我们坚信每个人都必须受到尊重，并且总是有更多考虑任何问题的方法。我们重视观点，思想，文化和观点的多样性。 7。财政责任：我们认为，稳固的财政管理是建立一所伟大大学的基础。 8.社会责任：我们认为知识是一种必须用来创造更美好世界的礼物。 9.对基本人权的承诺：最重要的是，我们重视每个人享有自由，尊重和实现其潜力的机会的权利。 AFFIRMATIVE ACTION Langston University, in compliance with Title VI and VII of the Civil Rights Acts of 1964, Executive Order 11246 as amended, Title IX of the Educational Amendments of 1972, Americans with Disabilities Act of 1990, and other federal laws and regulations, does not discriminate on the basis of race, color, national origin, sex, age, religion, handicap, or status as a veteran in any of its policies, practices,或程序。这包括但不限于招生，就业，经济援助和教育服务。 ADA声明Langston University完全订阅了1990年《美国残疾人法》（ADA）的所有必需标准。需要帮助的人应联系学生事务办公室的ADA合规官，第119室，Page Hall，[phone]。应在第一个预定课程期间，期间或之后的某个时刻进行报告，以便为学生在该课程中取得成功提供住宿。时间表：周期材料涵盖1 8/20 21-AUG生物信息学简介和教职员工的引入。刘易斯22-AUG 23-AUG DOE电影，并在计算机DR上安装程序。刘易斯24-AUG 2 8/27 28-AUG DNA，基因，蛋白质生物学概述-dr。 Aquaaah 29-Aug 30-Aug DNA，基因，蛋白质生物学概述-DR。 Aquaaah 31-AUG 3 9/3劳动节假期4-Sep Genomes-Dr。路易斯5-SEP 6-SEP基因组-DR。哑光/动手练习MR。 Depona 7-Sep 4 9/10 11-Sep新序列分析-DR。 Lewis，Bucki博士12-Sep 13 Sep新序列分析-DR。哑光/动手练习MR。 Depona 14-Sep 5 9/17 18-Sep成对对齐和序列数据库搜索：算法-DR。休·尼古拉斯（Hugh Nicholas）19-Sep 20-Sep评估-DR。吉米·托雷斯（Jimmy Torres）/动手练习-MR。 Depona 21-Sep 6 9/24 25-Sep数据库_search_signific-dr。 Lewis，Bucki博士26-Sep 27-Sep Database_search_sementific-dr。哑光/动手练习MR。 Depona 28-Sep 7 10/1 2-OCT数据库_SEREARCH-MATRICES-DR。 Matand 3-OCT 4-OCT应用数据库搜索-DR。刘易斯，动手练习。 depona 5-OCT归乡休息8 10/8归乡9-OCT Mutiple序列比对。 Hugh Nicholas-PSC 10-OCT期中考试期11-OCT Mutiple序列比对示例-DR。 Hugh Nicholas-PSC 12-OCT 9 10/15 16-OCT多序列对齐动手动手-Alex Ropelewski 17-OCT 18-OCT数学方法介绍 - DePona先生19-OCT 10 10/22 23-OCT计算生物学模型和BioInformatics-Mr中的数学模型入门。 Depona，动手练习MR。 Depona 24-OCT 25-OCT动手练习MR。 Depona 26-OCT 11 10/29 30-OCT醛脱氢酶基序，生物信息学，结构，功能和遗传学DR。 Accualaah 31-OCT 1-NOV动手练习MR。 Depona 2-NOV 12 11/5 6-NOV的同工酶-DR分析。 Aquaaah 7-nov 8-nov您的项目9-NOV 13 11/12 13-NOV您的项目14-NOV 15-NOV您的项目16-NOV 14 11/19 20-NOV您的项目21-NOV昨天丢下课程并接受了