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Summary Executive DRAFT April 20, 2005 The Case to Increase the Support of Doctoral Students Across the New Brunswick-Piscataway Campus of Rutgers, The State University of New Jersey Jolie A. Cizewski and Harvey Waterman The Graduate School New Brunswick Graduate student education and research are central to the mission of a research university and a measure of the excellence of that institution. Doctoral students are students first, and it is the responsibility of a research university and graduate programs to provide them with the background and guidance they need as they evolve into scholars. Graduate students play important roles in the research mission of the University and help to recruit and retain researchactive faculty members who want to work with and teach talented graduate students. At the same time, graduate students serve as instructors of undergraduates in laboratory, discussion, and skill sections of introductory courses, with the most experienced graduate students developing their own advanced courses for undergraduates. Often graduate students also participate in the service mission of the University. Graduate students bring enthusiasm and intellectual vitality to the university community and models of success for undergraduate students. Not least, the graduate students go forth to take up positions in industry, government, and academia from which they not only contribute to society but also refer others back to the place in which they did their graduate work. They become some of our best recruiters of future graduate students and advocates of our research. The graduate students who play some of the most central roles are those working toward the Ph.D. degree. They are highly recruited nationally and internationally. It typically takes five to seven years of full-time study and research to complete a Ph.D. degree, requiring graduate students to put future careers on hold. Few students have the personal or family resources to support themselves for so long, while simultaneously maintaining the immersion in their studies necessary for their full development as independent researchers and teachers. For that reason, at all research universities, it is considered essential that full support for at least five or six years be provided to doctoral students. Given the cost of living, the alternative paths students can choose, and the international competition for these students, the support provided must meet minimal standards for decent maintenance, health insurance, and remission of tuition and fees. However, at Rutgers, and in particular on the New Brunswick/Piscataway campus, graduate education faces considerable challenges because of the quality and quantity of support provided to graduate students at all stages of their studies. These challenges not only compromise our ability to rise to the next tier of public research universities, but if not corrected may compromise our ability to sustain the current level of excellence. This report documents the need to enhance the support of Ph.D. students in all forms, throughout their careers as students, across the New Brunswick/Piscataway campus, and proposes a timeline for significant increases in the quality of support we provide. The arguments address concerns shared by deans and faculty members across the campus, and include data from programs at peer AAU research universities. 1 Executive Summary DRAFT April 20, 2005 A. Principles and Challenges The following goals guide the case we are making to enhance the financial support of Ph.D. (doctoral) students: o Provide compensation packages, including medical benefits and tuition and fee remission, sufficient to enable doctoral students to live decently in the local area, for the duration of a typical course of study, with minimal impediments to focusing on their studies and research; o Provide compensation packages and funds to recruit doctoral students that address the competitive pressures we face and enable us to attract the most talented candidates for doctoral studies; o Remove barriers that deter faculty members from supporting doctoral students on external grants and contracts, including training grants; o Provide sufficient resources to ensure that all doctoral students can be offered at least minimal teaching experiences. There are several challenges to following these guidelines: o High cost of living in the New Brunswick/Piscataway area and on campus Currently, on-campus housing for a single graduate student is 44% of the gross minimum salary of a teaching or graduate assistant. On-campus housing costs increase much faster than the cost of living in the local community, averaging 7% per year in recent years. o Insufficient resources to support Ph.D. students on University fellowships Only a fraction of first-year, and a tiny fraction of dissertation-year, Ph.D. students are currently supported on fellowships. Because the budgets for fellowship stipends have not risen as rapidly as the increases in the cost of living and the stipends in peer programs, the number of students supported on University fellowships has decreased over the past decade, as resources are cannibalized to offer fewer students fellowships with higher stipends. Additional funds are needed in the very near term to sustain minimum stipend levels above the cost of living, provide stipends that meet the competition, provide health benefits for fellows, and to provide fee remission (or to provide higher stipends to compensate for lack of fee remission). In the longer term, additional funds are needed to increase the number of students supported on fellowships in their first, and in many disciplines also the final, years of study. 2 Executive Summary DRAFT April 20, 2005 o Insufficient number of teaching assistant positions Teaching assistants (TAs) play a central role in the delivery of undergraduate education at a research university, providing trained and committed instructors for discussion, laboratory and skills sections associated with large courses. Experienced TAs often teach their own courses. Support as a TA is also a key component of graduate student support, complementing support on a fellowship or on a research grant, providing the scholar in training with the skills required for success within the academy, as well as outside of the academy where a high level of communication skills is expected. However, at Rutgers we lag far behind our peer AAU public universities in the ratio of TA to tenure-track faculty positions. Many units do not have the resources to offer the small sections normally associated with large undergraduate courses that would ideally complement the lecture format. Much of the current teaching small-section is being done by part-time-lecturers, who often are graduate students who may not have the benefit of close interaction with faculty members that teaching assistants enjoy. Finally, we are far from the number of TA positions needed to encourage all Ph.D. candidates to have a teaching experience as part of the requirement for the degree. o Insufficient number of graduate students supported on research and training grants Support on external grants, either as a graduate research assistant (GA) or on a training grant, is also an important component of doctoral student support, especially in the sciences and engineering. However, the cost to support a GA on an external grant is perceived to be high, because to support a GA requires salary and fringe benefits and overhead, as well as tuition and fee remission, with tuition charged quite often at the non-resident rate. Therefore, faculty investigators either find it difficult to identify sufficient resources to provide the full support for a GA, or prefer to support a post-doctoral scholar. An alternative form of external support is via a training grant, but faculty members often find it difficult to develop successful, competitive proposals for such funding. Therefore, it is appropriate to reduce the barriers and thereby encourage more faculty members to support graduate student GAs on their grants, as well as provide the infrastructure to help them develop competitive training grant proposals. o Insufficient resources to recruit top doctoral students and support their research and studies Currently there is a very small investment in funds to recruit new doctoral students, including those with backgrounds that have traditionally been under-represented in graduate education and research. To attract these students requires funds to bring them to campus, as well as to provide packages of support that are competitive with peer programs at other institutions. These support packages must include not only 5 or 6 years of basic support, but must also include opportunities for support during the summer, modest research accounts, and access to funds to support their travel, for example to develop dissertation proposals or for archival or field special study or to present their research at professional conferences. 3 Executive Summary DRAFT April 20, 2005 B. Proposal to enhance support for doctoral students over the next decade The elements of our proposal include the following key items: o Increase by at least 250 the number of TA positions in New Brunswick/Piscataway This proposal could be realized by providing tuition and fee remissions and extra monies to existing state lines, as well as making the case to the State for additional lines to enhance the delivery of undergraduate education. At the same time the salaries, including competitiveness pool enhancements, would need to increase to compensate for increases in the local cost of living. o Adopt policies and resources designed to increase the number of doctoral students supported on external research and training grants This proposal could be realized by communicating realistic costs of supporting a graduate student, and at least some reductions in the tuition and fee charges, including only charging instate tuition for students supported on external grants. In addition, sufficient tuition remission resources would need to be available to provide remission when a funding agency does not provide such remissions or when support for an individual student is coming from several sources. To encourage training grant applications, a grants specialist should be supported who would work closely with the Graduate School and individuals or groups of faculty members in developing competitive proposals. o Dramatically increase resources to support graduate students on fellowships: To sustain stipends at competitive levels, To provide health benefits and fee remission, To increase the number of fellowships. The first phase of the proposal would be to provide sufficient resources to sustain stipends above the cost of living, and to start to address stipend pressures in the most competitive programs. This phase needs to be enacted immediately to stop the erosion of the number of students supported on fellowships. At the same time, health benefits for all fellows need to be phased in over the next few years, as recommended by several university committees. In future years, we propose to start to increase the number of fellowships towards the goal that all first year Ph.D. students would be supported on fellowships, with a sufficient number of dissertation fellowships to meet the needs in appropriate disciplines. Funds for new fellowships would come from a dramatic increase in endowed funds for graduate student fellowships, targeted in the next capital campaign, as well as University resources. o Increase funds to recruit high-quality doctoral students and support their research and study: Funds for programs to support on-campus visits and other recruiting activities for prospective students, 4 Executive Summary DRAFT April 20, 2005 Funds to enhance support packages, including summer support and research accounts, for students in competitive programs for which this is the national norm, Travel funds for pre-dissertation research or special study and conference travel. We propose that the University significantly enhance its investment in doctoral education by providing considerably more funds to recruit highly-talented students to the most Ph.D. competitive programs. Such funds would include direct support of program efforts to recruit new Ph.D. students, including bringing prospective students to campus, as well as supplemental funds to enhance support packages, such as summer compensation or research accounts, that address competitive pressures. Additional funds to support travel could come from increases in private funds associated with the next capital campaign. C. Ten years from now When this proposal to increase the support of Ph.D. students is realized, we will have increased our success in attracting the top doctoral students to our programs of highly-talented faculty members, while at the same time attracting and retaining faculty members who want to work with these students. Our Ph.D.s will then go on to faculty positions or work in the research institutes at the frontiers of discovery or serve in government or industry or non-profit organizations. Their success, in turn, will help to attract future cohorts of doctoral students who will repeat the cycle. In this way, Rutgers New Brunswick will come to be recognized as one of the top public research universities. 5
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Rutgers >> ECE >> 572 (Fall, 2008)
A Perspective on the Future of Massively Parallel Computing: Fine-Grain vs. Coarse-Grain Parallel Models Comparison & Contrast Predrag T. Tosic Open Systems Laboratory, Department of Computer Science, University of Illinois at Urbana Champaign (UIUC)...
Rutgers >> ECE >> 572 (Fall, 2008)
Parallel Architectures MICHAEL J. FLYNN AND KEVIN W. RUDD Stanford University flynn@Umunhum.Stanford.edu ; kevin@Umunhum.Stanford.edu PARALLEL ARCHITECTURES Parallel or concurrent operation has many different forms within a computer system. Using a...
Rutgers >> ECE >> 572 (Fall, 2008)
A Survey of Commercial Parallel P r o c e s s o r s Edward F. Gehringer Janne Abullarade Michael H. Gulyn Computer Systems Laboratory North Carolina State University Raleigh, NC 27695-7911 Abstract This paper compares eight commercial parallel proce...
Rutgers >> ECE >> 572 (Fall, 2008)
Task Assignment in a Distributed System: Improving Performance by Unbalancing Load Department of Computer Science Boston University Boston, MA 02215 Mark E. Crovella Laboratory for Computer Science MIT, NE43-340 Cambridge, MA 02139 Mor Harchol-Balt...
Rutgers >> ECE >> 572 (Fall, 2008)
Task Assignment with Unknown Duration MOR HARCHOL-BALTER Carnegie Mellon University, Pittsburgh, Pennsylvania Abstract. We consider a distributed server system and ask which policy should be used for assigning jobs (tasks) to hosts. In our server, j...
Rutgers >> ECE >> 572 (Fall, 2008)
The Load Rebalancing Problem Gagan Aggarwal gagan@cs.stanford.edu Rajeev Motwani rajeev@cs.stanford.edu Department of Computer Science Stanford University Stanford, CA 94305 An Zhu anzhu@cs.stanford.edu ABSTRACT In the classical load balancin...
Rutgers >> ECE >> 572 (Fall, 2008)
Low Contention on Load Balancing Large-Scale Maurice Herlihy * Multiprocessors Beng-Hong Lim t Nir Shavit $ Abstract 1 Introduction load balancing of parallel algorithm high levels levels can have a dramatic Designing because it Such since ty...
Rutgers >> ECE >> 572 (Fall, 2008)
Processor Allocation Policies for Message-Passing Cathy McCann of Computer of Parallel Computers and John Zahorjan and Engineering Department Science Washington 98195 University Seattle, WA mccann, zahorjan(lcs. Washington.edu Abstract...
Rutgers >> ECE >> 572 (Fall, 2008)
Effective Andrea Distributed C. Dusseau, Scheduling Remzi H. Arpaci, of Parallel Workloads E. Culler and David Computer University {dusseau, remzi, Science of California, Division Berkeley EDU culler}@CS.Berkeley. Abstract We present a dis...
Rutgers >> ECE >> 572 (Fall, 2008)
Demand-based Coscheduling of Parallel Jobs on Multiprogrammed Multiprocessors Patrick G. Sobalvarro pgs@lcs.mit.edu weihl@lcs.mit.edu William E. Weihly Abstract We present demand-based coscheduling, a new approach to scheduling parallel computation...
Rutgers >> ECE >> 572 (Fall, 2008)
Improving the Scalability of Parallel Jobs by adding Parallel Awareness to the Operating System June 30, 2003 Terry Jones, Shawn Dawson, Rob Neely William Tuel, Larry Brenner, Jeffrey Fier, Robert Blackmore, Patrick Caffrey International Business M...
Rutgers >> ECE >> 572 (Fall, 2008)
Pipeline and Batch Sharing in Grid Workloads Douglas Thain, John Bent, Andrea C. Arpaci-Dusseau, Remzi H. Arpaci-Dusseau, and Miron Livny Computer Sciences Department, University of Wisconsin, Madison Abstract We present a study of six batch-pipeline...
Rutgers >> ECE >> 572 (Fall, 2008)
Scheduling of Parallel Jobs in a Heterogeneous Multi-Site Environment Gerald Sabin, Rajkumar Kettimuthu, Arun Rajan and P Sadayappan The Ohio State University Columbus OH 43201 {sabin, kettimut, rajan, saday}@cis.ohio-state.edu Abstract Most previou...
Rutgers >> ECE >> 572 (Fall, 2008)
Scheduling Optimization for Resource-Intensive Web Requests on Server Clusters Huican Zhu, Ben Smith, Tao Yang Department of Computer Science University of California Santa Barbara, CA 93106 {hczhu, besmith, tyang} @cs.ucsb.edu Abstract Clustering s...
Rutgers >> ECE >> 572 (Fall, 2008)
...
Rutgers >> ECE >> 572 (Fall, 2008)
MPICH-V2: a Fault Tolerant MPI for Volatile Nodes based on Pessimistic Sender Based Message Logging Aur lien Bouteiller* , Franck Cappello* , Thomas H rault* , e e G raud Krawezik* , Pierre Lemarinier* , Fr d ric Magniette* e ee * LRI, Universit de ...
Rutgers >> ECE >> 572 (Fall, 2008)
CoCheck: Checkpointing and Process Migration for MPI Georg Stellner Institut f r Informatik der Technischen Universit t M nchen u au Lehrstuhl f r Rechnertechnik und Rechnerorganisation u D-80290 M nchen u stellner@informatik.tu-muenchen.de Abstract...
Rutgers >> ECE >> 572 (Fall, 2008)
MPI/FTTM: Architecture and Taxonomies for Fault-Tolerant, Message-Passing Middleware for Performance-Portable Parallel Computing* Rajanikanth Batchu, Jothi P. Neelamegam, Zhenqian Cui, Murali Beddhu, Anthony Skjellum, Yoginder Dandass, Manoj Apte MP...
Rutgers >> ECE >> 572 (Fall, 2008)
...
Rutgers >> ECE >> 572 (Fall, 2008)
E L SE VI E R SC I E N C E B . V. JOURNAL PAGES [DTD 1658 4.2.0] P A RC O ARTICLE No. PARCO 1658 PROD. TYPE: 01-17 DISPATCH 2 0 J un e 2 0 0 1 F RO M D IS K A Parallel Computing 000 (2001) 000000 www.elsevier.com/locate/parco 2 3 4 5 6 7...
Rutgers >> ECE >> 572 (Fall, 2008)
Fault Tolerance in MPI Programs William Gropp and Ewing Lusk Mathematics and Computer Science Division Argonne National Laboratory Argonne, IL 60439, USA {gropp,lusk}@mcs.anl.gov Abstract. This paper examines the topic of writing fault-tolerant MPI ...
Rutgers >> ECE >> 572 (Fall, 2008)
MPICH-V: Toward a Scalable Fault Tolerant MPI for Volatile Nodes George Bosilca, Aurelien Bouteiller, Franck Cappello, Samir Djilali, Gilles Fedak, Cecile Germain, Thomas Herault, Pierre Lemarinier, Oleg Lodygensky, Frederic Magniette, Vincent Neri, ...
Rutgers >> ECE >> 572 (Fall, 2008)
Sensor Network-Based Countersniper System Gyula Simon Gyrgy Balogh Gbor Pap Mikls Marti Branislav Kusy Jnos Sallai kos Ldeczi Andrs Ndas Ken Frampton Institute for Software Integrated Systems Vanderbilt University 2015 Terrace Place, Nashville, TN 3...
Rutgers >> ECE >> 572 (Fall, 2008)
A Wireless Sensor Network For Structural Monitoring Ning Xu Sumit Rangwala Alan Broad Krishna Kant Chintalapudi Deepak Ganesan Ramesh Govindan Deborah Estrin ABSTRACT Structural monitoringthe collection and analysis of structural resp...
Rutgers >> ECE >> 572 (Fall, 2008)
Power Conservation and Quality of Surveillance in Target Tracking Sensor Networks Chao Gui and Prasant Mohapatra Computer Science Department University of California, Davis Davis, CA 95616 {guic,prasant}@cs.ucdavis.edu ABSTRACT Target tracking is ...
Rutgers >> ECE >> 572 (Fall, 2008)
Energy-Efcient Surveillance System Using Wireless Sensor Networks Tian He, Sudha Krishnamurthy, John A. Stankovic, Tarek Abdelzaher, Liqian Luo, Radu Stoleru, Ting Yan, Lin Gu Department of Computer Science University of Virginia, Charlottesville, V...
Rutgers >> ECE >> 572 (Fall, 2008)
Building Efcient Wireless Sensor Networks with Low-Level Naming John Heidemann Ramesh Govindan Fabio Silva Chalermek Intanagonwiwat Deborah Estrin Deepak Ganesan Computer Science Department University of California, Los Angeles Los Angeles, CA, US...
Rutgers >> ECE >> 572 (Fall, 2008)
A Sensor Network Application Construction Kit (SNACK) Ben Greenstein Eddie Kohler Deborah Estrin University of California, Los Angeles {ben, kohler, destrin}@cs.ucla.edu ABSTRACT We propose a new conguration language, component and service library, ...
Rutgers >> ECE >> 572 (Fall, 2008)
Mat: A Tiny Virtual Machine for Sensor Networks e Philip Levis and David Culler {pal,culler}@cs.berkeley.edu Computer Science Division Intel Research: Berkeley University of California Intel Corporation Berkeley, California Berkeley, California ABST...
Rutgers >> ECE >> 572 (Fall, 2008)
Hood: A Neighborhood Abstraction for Sensor Networks Kamin Whitehouse Cory Sharp Eric Brewer David Culler {cssharp,kamin,brewer,culler}@cs.berkeley.edu Department of Electrical Engineering and Computer Science University of California, Berkeley Ber...
Rutgers >> ECE >> 572 (Fall, 2008)
The Dynamic Behavior of a Data Dissemination Protocol for Network Programming at Scale Jonathan W. Hui Computer Science Division University of California at Berkeley Berkeley, CA 94720 David Culler Computer Science Division University of California ...
Rutgers >> ECE >> 572 (Fall, 2008)
Matching Data Dissemination Algorithms to Application Requirements John Heidemann Fabio Silva Deborah Estrin USC/Information Sciences Institute Computer Science Department 4676 Admirality Way Marina del Rey, CA, USA 90292 {johnh,fabio}@i...
Rutgers >> ECE >> 572 (Fall, 2008)
Design and Implementation of a Framework for Efficient and Programmable Sensor Networks Abstract Wireless ad hoc sensor networks have emerged as one of the key growth areas for wireless networking and computing technologies. So far these networks/s...
Rutgers >> ECE >> 572 (Fall, 2008)
Directed Diffusion: A Scalable and Robust Communication Paradigm for Sensor NetworksIntanagonwiwat USC/Inforrnation Sciences Institute intanago@isi.edu Chalermek Ramesh Govindan USC/Information Sciences Institute govindan@isi.edu Deborah Estrin US...
Rutgers >> ECE >> 572 (Fall, 2008)
: :\' :\'~\':\'%\'.\" \".\'.:;~.\'.\".\":.\'.\':\':.:;~ ~:~$~\" v\'.:i.\':j~!.\'.\'~\" \".\', .~ i : i.: : :: : :.: :.:.~.:.\'~.:!k:~.:~\'.\"~: .:~.: = : . \":\'~\':\" :~*:f.~\'~i:~:~\'-\'~*:.*:*:.\':\':\': ~.:.:.~.:. ~ . :\":\': .: .:. :.:.+ .:.-:.:.:.: ~ ~:\':\'$~:~ ~.~.~\'~\'~,.~.,~.\" ....
Rutgers >> ECE >> 572 (Fall, 2008)
An Evaluation of Multi-resolution Storage for Sensor Networks Deepak Ganesan Ben Greenstein Denis Perelyubskiy Deborah Estrin John Heidemann Department of Computer Science, UCLA, Los Angeles, CA 90095 USC/ISI, 4676 Admiralty Way, Marina Del Rey, ...
Rutgers >> ECE >> 572 (Fall, 2008)
Appearing in 5th Annual Symposium on Operating Systems Design and Implementation (OSDI). December, 2002. 1 Samuel Madden, Michael J. Franklin, and Joseph M. Hellerstein madden,franklin,jmh @cs.berkeley.edu UC Berkeley Abstract We present the Tiny A...
Rutgers >> ECE >> 572 (Fall, 2008)
To appear, ACM SenSys 2004 ELF: An Efcient Log-Structured Flash File System For Micro Sensor Nodes Hui Dai Michael Neufeld Richard Han University of Colorado at Boulder Computer Science Department Boulder, CO, 80302 {huid, neufeldm, rhan}@cs.color...
Rutgers >> ECE >> 572 (Fall, 2008)
DFuse: A Framework for Distributed Data Fusion * Rajnish Kumar, Matthew Wolenetz, Bikash Agarwalla, JunSuk Shin, Phillip Hutto, Arnab Paul, and Umakishore Ramachandran {rajnish, wolenetz, bikash, espress, pwh, arnab, rama}@cc.gatech.edu College of Co...
Rutgers >> ECE >> 572 (Fall, 2008)
MANTIS: System Support for MultimodAl NeTworks of In-situ Sensors H. Abrach, S. Bhatti, J. Carlson, H. Dai, J. Rose, A. Sheth, B. Shucker, J. Deng, R. Han University of Colorado at Boulder Department of Computer Science Contact author: rhan@cs.colora...
Rutgers >> ECE >> 572 (Fall, 2008)
Decentralized Aggregation Service in Sensor-based Pervasive Environments Course Project Report, Spring 2005 Nanyan Jiang Abstract For emerging applications in sensor and RFID based pervasive environment, the main data ow is from many devices at the ...
Rutgers >> EDEN >> 2 (Fall, 2008)
KEEPING UP WITH CP Taking the Dis out of Disability by: Paul Stuart Wichansky Its amazing what you can do with a positive attitude. When I started learning to walk at seven years old, many orthopedists who examined me believed that I would never be ...
Rutgers >> MBB >> 215 (Fall, 2008)
Introduction to Vectors In order to study a DNA fragment (e.g., a gene), it needs to be amplied and eventually puried. These tasks are accomplished by cloning the DNA into a vector. A vector is generally a small, circular DNA molecule that replicates...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: Sequencing DNA Size? Determine the size of the insert Sequencing DNA First developed in the mid 1970\'s. Before this time the actual nature of genes was still largely a mystery. As 1968, all the genetic code had not been solved. 1995 -...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: Cropping and editing DNA sequences Link to Sequence Files p. 3-10 Sequences for clone 1AG1.07 SP XP What do I do with this? 4-3 Link to DSAP Log in to DSAP (Register if first time user) p. 4-4 Clone status page p. 4-5 List of cl...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: BLASTX Why do a BLASTX if we have done a BLASTN? BLASTN Match Query Sbjct AGG TCG TTA CTA TCG AGG AGT AGA | | | | CGT AGC CTT TTG AGT CGA TCG CGG 16% Identity R S L L S RS R AGG TCG TTA CTA TCG AGG AGT AGA | | | | CGT AGC CTT TTG AGT CGA ...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch10: Literature Analysis p. 10-1 p. 10-2 p. 10-2 p. 10-2 Wikipedia - p. 10-3 p. 10-3 p. 10-4 p. 10-4 p. 10-5 p. 10-6 p. 10-7 p. 10-8 p. 10-8 p. 10-9 ...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch12: Spanning the gap between sequences No overlap between the SP and XP sequences p.12-1 How Big? A) Estimate the size of the gap from the size of the insert determined by agarose gel electrophoresis 1) Sequenced 1470 bp (SP + XP) 2) Determined ...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch13: Giving a Research Presentation Goal of a research talk Primary goal for a scientific presentation is to inform or persuade an audience about technical results Clarity Deliver the information in as logical and straightforward a fashion as possi...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch 15: Undergraduate Research Ch 16: Career Options Advantages of undergraduate research Required for MBB (694) Genetics (447) majors Helps with course work Easy A (have to put in the time, but no exams) Learn to navigate RU from upper classmen Par...
Rutgers >> MBB >> 215 (Fall, 2008)
MBB Curriculum - Make research and course work synergistic activities Learn science by doing science All MBB majors required to do independent research projects Can choose from over 300 faculty on RU/UMDNJ campus 315 Goal: To introduce students to ba...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 0 - The Basics Chapter 1 The Basics: DNA, RNA, Proteins, Transcription, and Translation Introduction In order to work in a modern molecular biology laboratory, it is essential that you know the basic biology of nucleic acids and proteins. Yo...
Rutgers >> MBB >> 215 (Fall, 2008)
The Basics: A general review of molecular biology: DNA Transcription RNA Translation Proteins DNA (deoxy-ribonucleic acid) is the genetic material -think of it as the blueprint DNA structure- a polymer of nucleotides Nucleotides have : 2) a ring-...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 1 Vectors and Libraries Chapter 1 Vectors and Libraries Information in this lecture was adopted from Chapter 7 in Introduction to Genetic Engineering by W. H. Sofer, Butterworth-Heinemann Publishing; An Introduction to Recombinant DNA Techn...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 3 Sequencing, Databases Chapter 3 Sequencing DNA and Databases Introduction One of the most remarkable scientific advancements in history is the molecular biology revolution. In 1953 James Watson and Francis Crick proposed a molecular struc...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: Editing DNA sequences p. 5-1 p. 5-1 Edit options in 4 Peaks p. 5-2 A dye blob at the beginning of the SP sequence Before Editing After Editing p. 5-2 Examples of sequences with background noise p. 5-3 Sequence that is not reliable...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 6 Analysis of XP, Determine Overlap, Make contig Chapter 6 I. Analysis of XP waveform II. Determine if the SP and XP sequences overlap III. Making a contig from the SP-XP Sequences I. Analysis of XP waveform The previous chapters went over ...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: Analysis of the XP sequence and forming a contig. Possible SP and XP overlaps p. 6-1 The XP sequence must go through a run of Ts. p. 6-1 Slipping of strands during DNA synthesis Length of DNA 5\'-TTTTTTTTTTTTTT N 3\'-AAAAAAAAAAAAAAAAAAAAA...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 8 BLASTX Chapter 8 BLASTX Analysis Search the NCBI database to determine if your gene codes for a protein that is found in other organisms. a. Background In the previous step you compared your DNA sequence with other DNA sequences in the NCB...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 9 Determine ORF, BLASTP Chapter 9 Determine the protein sequence coded by your gene. a. Background In the last step, you searched the protein databases for matches to peptide sequences generated from all 6 reading frames of your cDNA. If yo...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 10 Literature Search Chapter 10 Search the literature and protein databases to determine the function of the protein coded by your gene. In the previous steps you analyzed the quality of your sequence then searched for homologs of the gene ...
Rutgers >> MBB >> 215 (Fall, 2008)
Lecture: ORF analysis and BLASTP p 9-1 p 9-1 p 9-2 Possible types of clones in the cDNA library p 9-2 Toolbox-2 DNA Sequence Translation Program p 9-3 Toolbox-2 DNA Sequence Translation Program p 9-3 BLASTX of EX1.06 p 9-4 Look for the fi...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 11 CLUSTALW, Structure Chapter 11 Further analysis of one clone: ClustalW and Structure analysis After performing the sequence analysis using DSAP on all your clones, you may want to choose one clone that you find interesting for a more det...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 12 Span the gap between sequences Chapter 12 Spanning the gap between the SP and XP sequences When you perform the BLAST2 sequence analysis with your SP and XP sequences you may get the result back that the two sequences do not overlap (Fig...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch11: CLUSTALW, Structure >A. franciscana MQIHLRGSDSSTQVINCDEGDCVIALKEQVAALEGVKVSEVRLFANGTPLTEDIPLNGIQDTIDFSVPLLGGKVHGSLARAGKVKGQTPK VDKQEKKKKKTGRCKRRIQYNRRFVNVCLQLFGP >D. cervinus 1 mqlhirgqss hvlecegtet igqlkaqiaa leqlnfdeis lysqgtpitd dsiastfdda ...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 13 Tools of Molecular Biology Chapter 13 Important Tools of Molecular Biology 1. Introduction Although a major focus in this course is directed towards isolating and sequencing cloned cDNAs, it is important to realize that the tools of mole...
Rutgers >> MBB >> 215 (Fall, 2008)
Ch13: Tools in Molecular Biology Blotting The transfer of biomolecules onto a membrane support 1) Preparing a cell-free extract containing the biomolecule(s) of interest 2) Resolve the mixture by gel electrophoresis 3) Transfer the gel onto a membra...
Rutgers >> MBB >> 215 (Fall, 2008)
Chapter 14 Presentations Chapter 14 Presentation Hints An important part of science is performing experiments to test your ideas and models or discover new information. However, an equally important part of science is being able to communicate your...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 1 Pipeting and dilutions Lab 1 I. Pipet bulbs: Each group will be given a black rubber bulb siphon to pipet liquids. These tools for measuring liquids from 1 to 25 ml are used in conjunction with pipets. The pipets used in the laboratory are st...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 3- Techniques Lab 3 Basic Techniques Demonstration of using a spectrophotometer, balances, and sterile technique. Expt. #3A: Dilute 10X TE Buffer to Make 1X TE Buffer Expt. #3B: Determine the Concentration of an Unknown DNA Sample Buffers Many o...
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