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					CSE/IT             MULTICORE TECHNOLOGIES                               L T P M
424(D)
                                                                        4   1   0   100
UNIT-I
INTRODUCTION TO MULTIPROCESSORS AND SCALABILITY:Scable design
principles – Principles of processor design – Instruction Level Parallelism, Thread
level parallelism. Parallel computer models –- Symmetric and distributed shared
memory architectures – Performance Issues, Brief introduction to cache hierarchy
and communication latency,Shared memory multiprocessors, General architectures
and the problem of cache coherence, Synchronization primitives: Atomic primitives;
locks: TTS, ticket, array;barriers: central and tree; performance implications in
shared memory programs;

UNIT-II
 Multi-core Architectures - Introduction to multi-core architectures -Software and
hardware multithreading – SMT and CMP architectures –Design issues – Case
studies – Intel Multi-core architecture – SUN CMP architecture., issues involved into
writing code for multi-core architectures, development of programs for these
architectures, program optimizations techniques, building of some of these
techniques in compilers/

UNIT III
PARALLEL PROGRAMMING :Fundamental concepts – Designing for threads –
scheduling - Threading and parallel programming constructs – Synchronization –
Critical sections – Deadlock. Threading, APIs, OpenMP – Threading a loop – Thread
overheads – Performance issues – Library functions. Solutions to parallel
programming problems – Data races, deadlocks and livelocks – Non-blocking
algorithms – Memory and cache related issues.

Unit-IV: Chip multiprocessors: Why CMP (Moore's law, wire delay); shared L2 vs.
tiled CMP; core complexity; power/performance; Snoopy coherence: invalidate vs.
update, MSI, MESI, MOESI, MOSI; performance trade-offs; pipelined snoopy bus
design; Memory consistency models: SC, PC, TSO, PSO, WO/WC, RC; Chip
multiprocessor case studies: Intel Montecito and dual-core, Pentium4, IBM Power4,
Sun Niagara

TEXTBOOKS:

1. Shameem Akhter and Jason Roberts, “Multi-core Programming”, Intel Press,
2006.
2. Michael J Quinn, Parallel programming in C with MPI and OpenMP, Tata Mc graw
Hill, 2003.

REFERENCES:

1. John L. Hennessey and David A. Patterson, “ Computer architecture – A
quantitative approach”, Morgan Kaufmann/Elsevier Publishers, 4th. edition, 2007.

2. David E. Culler, Jaswinder Pal Singh, “Parallel computing architecture : A
hardware/ software approach” , Morgan Kaufmann/Elsevier Publishers, 1999
                                         100
CSE/IT            BIOINFORMATICS                                  L T P        M
425(A)
                                                                   4   1   0   100

UNIT – I                                                      (15 Periods)
  1. Introduction
      Definitions, Sequencing, Molecular Biology and Bioinformatics, Biological
      sequence/structure, Genomoe Projects, Pattern Recognition and prediction,
      Folding problem, Sequence Analysis, Homology and Analogy, Bioinformatics
      Applications, Central Dogma of Molecular Biology
  2. Information Resources
      Biological databases, Primary Sequence databases, Protein sequence
      databases, Secondary databases, Protein pattern databases, and Structure
      classification databases DNA sequence databases, specialized genomic
      resources

UNIT – II                                                       (18 Periods)
  3. DNA Sequence Analysis
      Importance of DNA analysis, Gene Structure and DNA sequences, Features
      of DNA sequence analysis, EST (Expressed Sequence Tag) searches, Gene
      Hunting, Profile of a cell, EST analysis, Effects of EST data on DNA
      databases, The Human Genome Project
  4. Pair Wise Alignment Techniques
      Database Searching, Alphabets and complexity, algorithm and programs,
      comparing two sequences, sub-sequences, Identity and similarity, The Dot
      plot, Local and Global similarity, Different alignment techniques, Scoring
      Matrices, Dynamic Programming, Pair wise database searching

UNIT – III                                                    (15 Periods)
  5. Multiple sequence alignment & Phylogenetic Analysis
      Definition and goal, The consensus, Computational complexity, Manual
      methods, Simultaneous methods, Progressive methods, Databases of
      Multiple alignments, and searching, Applications of Multiple Sequence
      alignment, Phylogenetic Analysis, Methods of Phylogenetic Analysis, Tree
      Evaluation, Problems in Phylogenetic analysis, Tools for Phylogenetic
      Analysis
  6. Secondary database Searching
      Importance and need of secondary database searches, secondary database
      structure and building a sequence search protocol

UNIT – IV                                                     (12 Periods)
  7. Gene Expression and Microarrays
      Introduction, DNA Microarrays, Clustering Gene Expression Profiles, Data
      Sources and tools, Applications
  8. Analysis Packages
      Analysis Package structure, commercial databases, commercial software,
      comprehensive packages, packages specializing in DNA analysis, Intranet
      Packages, Internet Packages.



                                      101
Text Book:
1. Introduction to Bioinformatics T K Attwood And D.J. Parry-Smith, Pearson
2. Bioinformatics methods and applications S.C. Rastogi, N. Mendiratta And
P.Rastogi., PHI
Reference Books:
1. Introduction to Bioinformatics Arthur M. Lesk OXFORD Publishers (Indian
    Edition)
2. Elementary Bioinformatics, Imtiyaz Alam Khan, Pharma Book Syndicate




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