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of art the state of the network. Then, all processes can independently of each other create a single process checkpoint. It is possible to either create a checkpoint of the complete application on disk or to migrate a subset of processes. In the case of migration the checkpoint is directly transfered to a skeleton process on the new host. Implementations for both tuMPI and PVM have been done. During the adaptation for MPI it turned out that modi cations to the sources were only necessary, when the processes re-enroll after restart. Apart from that porting CoCheck to MPI was not more dif cult than porting any other parallel application. To obtain the software refer to the CoCheck homepage: The http://wwwbode.informatik.tu-muenchen.de/CoCheck performance of migration is determined by the main memory size of the process to be migrated. Other factors, like the number of processes or the communication/computation ratio proved to be negligible. The major limiting factor is the speed of the underlying network. As a consequence, high-speed interconnects could further reduce migration times. Future research will be going in several directions. First, CoCheck s usability as a global scheduler for resource management systems will be evaluated. Therefore, an integration of CoCheck into existing resource managers is planed. 763 (1)
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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...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 4- Making ON Cultures Lab #4: Setting up Overnight Cultures of Bacteria 1. Analyze the results from the library that you plated last week. You should think about and answer the following questions. i) Are there cells on the plate? ii) Is the pl...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 5 - Minipreps Lab #5 Plasmid DNA Minipreps Samples You will purify plasmid DNA from the bacterial cultures you started in the previous lab. Below is the protocol to do this. This is the same protocol described in Chapter 1, although most of the ...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 6 Restriction Digests & PCR Lab 6 Restriction Digests and PCR of Plasmid Samples Expt #1. Restriction Mapping of cDNA Library Plasmid DNA 1. Thaw your plasmid DNA samples from Week 3 Lab by taking them out of your styrofoam box and placing them ...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 7 Preparing and running an Agarose Gel Lab 7 Preparing and running an Agarose Gel 7A) Prepare the agarose gel. 1. Each group should prepare two liters of 1X TBE buffer containing 0.5 g/ml ethidium bromide. The 10X TBE stock is located in bottles...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 8 DNA Sequencing Reactions Lab 8 DNA Sequencing Reactions By this point you have performed restriction digests and PCR on 4 clones from the DNA library and run them on the agarose gel. You should determine the size of the inserts for each clone...
Rutgers >> MBB >> 215 (Fall, 2008)
Lab 9 Deletion Subcloning Lab 9 Deletion subcloning of a plasmid from the Artemia cDNA Library Expt 9.A: Restriction digest of plasmid DNA/ Verify on an agarose gel Expt 9.B: Ligation of the restriction digest Expt 9.C: Transformation of the ligatio...
Rutgers >> MBB >> 215 (Fall, 2008)
215 Clone Management Log Sheet BLASTN NCBI Clone Name Date of Insert ON Size Culture (bp) SP Seq. Access. Date # Name BLASTX NCBI E Access. val. # Name E XP # XP val. Sequ Overl ence ap Date with SP Supplement 1 Supplement 1 Clone Name: Group: Cl...
Rutgers >> MBB >> 215 (Fall, 2008)
215 Clone Management Log Sheet BLASTN NCBI Clone Name Date of ON Culture Insert Size (bp) SP Seq. Date Access. # Name E Access.# val. BLASTX NCBI Name E val. XP # XP Seque Overl nce ap Date with Supplement 1 ...
Rutgers >> MBB >> 215 (Fall, 2008)
Intro to Research 315 Quiz 1 20 points total 9/12/06 Name_ Group #_ 1. (2 points) Fill in the DNA complement of the rest of this strand. Indicate both the 5\' and 3\' ends of the new strand. 5-A T T C G C A C T G-3\' 3-T A A G C G T G A C-5\' 2. (2...
Rutgers >> MBB >> 215 (Fall, 2008)
Intro to Research 215 Quiz 1 20 points total 9/11/07 Name_ Group #_ 1. (2 points) Fill in the DNA complement of this strand. Indicate both the 5\' and 3\' ends of the new strand. 5-A T T C G C A C T G-3\' 3-T A A G C G T G A C-5\' 4. (6 points) DNA ...
Rutgers >> MBB >> 215 (Fall, 2008)
Intro to Research 215 Quiz 1 20 points total 9/9/08 Name_ Group # (2 points) _ Please address with short answers: 1) What experiments will you be doing in the lab this week (6 points)? A. Making 1X TE B. Determining the concentration of DNA by ab...
Rutgers >> MBB >> 215 (Fall, 2008)
IMBBR 315 Quiz #2 Sept 19, 2006 Name_ Group _ 1. (2 points) What is the main experiment you will perform in lab this week? We will be doing minipreps to make DNA from the colonies we picked last week. 2. (3 points) Briefly explain why it is import...
Rutgers >> MBB >> 215 (Fall, 2008)
694-215 Quiz 2 Vectors & Minipreps 9/16/08 Name: _ Group _ 1. (4 points) What are vectors used for? A vector is a DNA molecule, such as a plasmid or virus genome, that can replicate in a host organism. DNA fragments of interest can be inserted (clon...
Rutgers >> MBB >> 215 (Fall, 2008)
Quiz #3 (Sept 26, 2006). Name_Group # _ 1. (4 pts) What are the two critical rules when working with enzymes? ? Keep them on ice Use a fresh tip each time. 2. (3 pts ) How do bacteria protect their DNA from the restriction enzymes that they produce? ...
Rutgers >> MBB >> 215 (Fall, 2008)
215-08 Quiz 3 RE/PCR Name: _ Section: _ 1. (6 points) You want to do an EcoRI digest of your plasmid. You want to cut 1 g of plasmid DNA with 10 Units of EcoRI enzyme in 1X Buffer 2 in a total digest volume of 20 l. Indicate the volume of each ingre...
Rutgers >> MBB >> 215 (Fall, 2008)
Restriction Digest and Mapping Problem Set Name _ Group _ 1. a) Using the chart provided in the NEB manual (or on-line), which buffer would you use to set up a digest with the following enzymes. Indicate any special additives or reaction conditions:...
Rutgers >> MBB >> 215 (Fall, 2008)
215 Midterm exam (Oct 24, 2006) NAME:_Group:_ NOTE: There are 12 questions in total (9 pages total) 1. (6 points) A scientist working at Merck is doing some minipreps and runs out of Buffer P2. Buffer 2 is 0.2 N NaOH and 1% SDS. It turns out that the...
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