INTRODUCTION TO BIOINFORMATICS

生物信息学导论

• 批准号: 8171946
• 负责人: Shalun Lewis
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171946
• 关键词: Absenteeism at work; Accountability; Admission activity; Age; Algorithms; Amendment; American; Arabidopsis; Area; Arts; Award; Bacillus subtilis; Base Sequence; Behavior; Bioinformatics; Biology; 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; 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

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 兰斯顿大学艺术与科学学院 生物系 生物信息学导论 BI4133 2007 年秋季学期 教师 Sharon Lewis 博士 - 307 Hamilton Hall - [phone] [e-mail] 办公时间：MW 10:00-3:00下午办公时间：周五晚上 10:00-12:00 George Acquaah 博士 404 研究大楼 - [phone] [e-mail] 办公时间：MWF 上午 10:00-11:00 Kanyand Matand 博士 235 研究大楼 - [phone] [e-mail] 办公时间：MWF 10-1:00下午Theophilus Depona 先生 - 219 Hamilton Hall [phone] [e-mail] 办公时间：MWF 下午 2-5 点办公时间：周四 上午 8 点至上午 10 点 组织讲座 实验室日 周二 周四 时间 1-2:15 1-2:15 Room Research Bldg, rm 405 HamH 316A 所需文本和材料 本课程将分配期刊文章。目录说明 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。兰斯顿大学来自不同学科（化学、生物学、数学、计算机科学和研究）的教师团队将教授这门课程，目标是培养研究型少数族裔学生从事生物信息学职业。有兴趣的学生可以竞争 PSC 的暑期实习机会。基本原理 生物信息学是人类基因组计划和此后不久万维网出现的结果而发展起来的一个研究领域。一旦聚合酶链式反应和DNA测序仪等专利技术被开发出来，分子生物学家就开始对从人类、大鼠和小鼠到水稻和拟南芥等植物，再到大肠杆菌和枯草芽孢杆菌等微生物的整个基因组进行测序。这位科学家很快意识到，需要有人提供工具来收集、存储和分析数量呈指数级增长的核苷酸序列。计算机科学家需要编写脚本来组装整个基因组并比较基因组内和基因组之间的基因（大鼠与人类与蚊子）。计算机科学家很快意识到需要数学家来处理统计、算法和矩阵的复杂细节。生物信息学是一个多学科领域，如果有的话，它会不断发展以满足后基因组领域的需求。 一、瞄准无限的个性化医疗领域。课程目标 学生应该： 1. 定义生物信息学并了解这门学科是如何发展的。 2. 完成 Unix 操作系统实践练习。 3. 从数据库中检索序列并完成实践练习。 4. 完成数据库搜索和对齐实践练习。 5. 完成多序列比对实践练习。 6. 完成模式识别与匹配 动手练习。 7. 完成 Python 练习。 8. 完成系统发育分析实践练习。 9. 完成在序列组中查找特征的动手练习。教学方法 本课程将由在其研究领域拥有丰富经验的教师团队授课。教师在展示他们的信息时将使用实践练习、PowerPoint 演示和期刊文章。课程要求 每个学生应该： 1. 准时参加所有课程。 2. 完成所有实践练习。参加所有考试或测验。 3. 完成您的项目。 4. 展示您的项目。评估方法 - 课程要求分数 每位教师将根据主题内容对学生进行评估。最低成绩要求：A = 90%； B=80%； C=70%； D=60%； F = 低于 59% 3. 课堂出勤 学生必须参加所有讲座和实验。每节课涵盖的材料是 至关重要，是后续材料的先决条件。错过一场讲座的材料会严重妨碍学生理解相关材料的能力。上课时将分发出勤表。每天上课。如果没有安排实验室作业，则课程将在背诵室举行。六 (6) 名缺席可能会导致行政退学。学术事务办公室将仅在以下两个方面给予缺席理由： 参与大学职能（谁是 足球队？），以及主治医生正式声明中记录的疾病。学术诚信——禁止作弊 以下内容适用于学术不诚实案件。教师通常对学生的成绩或因作弊或抄袭而降低成绩拥有最终决定权。如果有明确且令人信服的证据表明发生了作弊或剽窃行为， a) 讲师将采取适当的学术纪律处分，其中可能包括 在特定作业或课程中获得“F”。 b) 讲师将向系主任、学术事务副校长、学生事务副校长和学生报告事件和采取的行动（如果有）。 c) 学生纪律委员会可以审查该事件并实施行为纪律，包括行为留校察看和停学。 d) 如果学生愿意，他/她可以与学生纪律委员会和/或学生司法法庭讨论此事。教室中电子设备政策 - 考试期间禁止手机响铃 所有电子设备（例如手机、寻呼机、掌上电脑、传呼手表）均被视为不必要的干扰，应在课堂上关闭并隐藏（手表除外）。因此，在课堂上与这些设备进行交互是不被容忍的。教师可以出于教学目的做出例外。预计发生紧急情况并希望在课堂上通过外部来源联系的学生必须直接通过每个校区指定的紧急调度系统。紧急调度员将接收消息并将其传递给教练。不遵守本政策的学生将首先被开除出班级，并且（根据教师的判断）可能会被计为缺席。在此期间错过的工作可能会被扣分。第二次违反此政策的学生将因破坏行为而被从课程中除名。在考试期间激活电子设备的学生将被开除出班级，并被剥夺完成或参加考试的机会。教师可以选择不对该考试进行评分。兰斯顿大学：愿景声明兰斯顿大学是一所历史悠久的黑人高等教育机构，将继续其丰富的传统，通过卓越的教学、研究、社区服务以及公共和私营部门的合作伙伴关系，从多元化、多文化的学生群体中培养领导者。随着兰斯顿大学从卓越走向伟大，它将因为俄克拉荷马州、美国和世界服务不足的人口所面临的问题提供解决方案而受到认可。兰斯顿大学：核心价值观 1. 强烈的职业道德和奉献精神：我们团结一致，尽一切努力和必要的时间努力工作，以实现我们的愿景，即为俄克拉荷马州、国家和世界上不值得的人口所面临的问题开发创造性的解决方案。 2. 对学习的热情：我们对知识的热情，我们对理解“为什么”的追求以及我们对开发创新答案的渴望，创造了一个充满活力的学术社区。 3. 勇于树立模范品格：我们正在建设一个教职员工和学生维护和重视高道德标准的社区。 4. 卓越：我们重视、珍惜并奖励在学术、教学和社区服务方面的卓越表现。 5. 学术创新和对学术的承诺：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. 欣赏差异：我们坚信每个人都必须受到尊重，并且考虑任何问题的方式总是不止一种。我们重视意见、想法、文化和观点的多样性。 7. 财政责任：我们相信，扎实的财政管理是建立一所伟大大学的基础。 8. 社会责任：我们相信知识是一份礼物，必须用来创造一个更美好的世界。 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。平权行动 兰斯顿大学遵守 1964 年民权法案第六章和第七章、经修订的第 11246 号行政命令、1972 年教育修正案第九章、1990 年美国残疾人法案以及其他联邦法律和法规，在其任何政策中不存在基于种族、肤色、国籍、性别、年龄、宗教、残障或退伍军人身份的歧视，实践， 或程序。这包括但不限于入学、就业、经济援助和教育服务。 ADA 声明 兰斯顿大学完全遵守 1990 年美国残疾人法案 (ADA) 的所有要求标准。需要帮助的人应联系学生事务办公室的 ADA 合规官员，地址：Room 119, Page Hall，电话 [phone]。应在第一个预定课程之前、期间或之后的某个时间报告此情况，以便为学生提供便利，以便在该课程中取得成功。时间表：每周日期 涵盖的材料 1 8/20 8 月 21 日 生物信息学简介和教员博士介绍。 Lewis 8 月 22 日 8 月 23 日 DOE 电影和在计算机上安装程序 - 博士。 Lewis 24-Aug 2 8/27 28-Aug DNA、基因、蛋白质生物学概述-博士。 Acquaah 8 月 29 日 8 月 30 日 DNA、基因、蛋白质生物学概述 - 博士。 Acquaah 31-8 月 3 9/3 劳动节假期 4-9 月 Genomes-Dr.刘易斯 5-9 月 6-9 月基因组-博士。 Matand/动手练习-Mr. Depona 7-Sep 4 9/10 11-Sep 新序列分析-Dr. Lewis, Bucki 博士 9 月 12 日 9 月 13 日新序列分析-Dr. Matand/动手练习-Mr. Depona 5 月 14 日 9/17 9 月 18 日 成对比对和序列数据库搜索：算法-Dr.休·尼古拉斯 9 月 19 日 9 月 20 日评估-博士。吉米·托雷斯/动手练习-先生。德波纳 6 月 21 日 9/24 9 月 25 日 Database_Search_Significance-Dr. Lewis，Bucki 博士 9 月 26 日 9 月 27 日 Database_Search_Significance-Dr. Lewis Matand/动手练习-Mr. Depona 28-9 月 7 10/1 2-10 月 Database_Search-Matrices-Dr. Matand 3-Oct 4-Oct 应用数据库搜索-Dr.刘易斯，动手练习-先生。 Depona 10 月 5 日返校休息 8 10/8 返校休息 10 月 9 日多重序列对齐 - 博士。 Hugh Nicholas-PSC 10-10 月期中考试期 11-10 月多序列对齐-示例-Dr. Hugh Nicholas-PSC 9 月 12 日 10/15 16 月多序列比对实践 Alex Ropelewski 10 月 17 日 18 月数学方法简介 - Depona 先生 10 月 19 日 10/22 10 月 23 日计算生物学和生物信息学数学模型简介 - 先生。德波纳，动手练习-先生。 Depona 24-Oct 25-Oct 实践练习-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-博士。 Acquaah 31-10 月 1-11 月实践练习-先生。 Depona 2-11 月 12 11/5 6-11 月同工酶分析-Dr. Acquaah 11 月 7 日 11 月 8 日 您的项目 11 月 9 日 13 月 13 日 11/12 11 月 13 日 您的项目 11 月 14 日 15 月 15 日 您的项目 16 月 14 日 11/19 11 月 20 日 您的项目 11 月 21 日 最后一天退课并获得