Escape analysis and lock coarsening in JAVA 6.0


The popularity of the Java programming language has made escape analysis a target of interest. Java's combination of heap-only object allocation, built-in threading, and the Sun HotSpot dynamic compiler creates a candidate platform for escape analysis related optimizations. Escape analysis is implemented in Java Standard Edition 6.


Example (Java)

class A {
  final int finalValue;
 
  public A( B b ) {
    super();
    b.doSomething( this ); // this escapes!
    finalValue = 23;
  }
 
  int getTheValue() {
    return finalValue;
  }
}
 
class B {
  void doSomething( A a ) {
    System.out.println( a.getTheValue() );
  }
}
In this example, the constructor for class A passes the new instance of A to B.doSomething. As a result, the instance of A—and all of its fields—escapes the scope of the constructor.

Java is able to manage multithreading at the language level. Multithreading is a technique that allows programs to operate faster on computer system that have multiple CPUs. Also, a multithreaded application has the ability to remain responsive to input, even when it is performing long running tasks.
However, programs that use multithreading need to take extra care of objects shared between threads, locking access to shared methods or blocks when they are used by one of the threads. Locking a block or an object is a time-consuming operation due to the nature of the underlying operating system-level operation involved .
As the Java library does not know which methods will be used by more than one thread, the standard library always locks blocks when necessary in a multithreaded environment.
Prior to Java 6, the virtual machine always locked objects and blocks when asked to by the program even if there was no risk of an object being modified by two different threads at the same time. For example, in this case, a local Vector was locked before each of the add operations to ensure that it would not be modified by other threads (Vector is synchronized), but because it is strictly local to the method this is not necessary:
public String getNames() {
     Vector v = new Vector();
     v.add("Me");
     v.add("You");
     v.add("Her");
     return v.toString();
}
Starting with Java 6, code blocks and objects are locked only when necessary , so in the above case, the virtual machine would not lock the Vector object at all

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Life Science Candidates can become Study Programmer's at Accenture, Chennai


Accenture is a global management consulting, technology services and outsourcing company. Combining unparalleled experience, comprehensive capabilities across all industries and business functions, and extensive research on the world’s most successful companies, Accenture collaborates with clients to help them become high-performance businesses and governments. With approximately 177,000 people serving clients in more than 120 countries, the company generated net revenues of US$21.58 billion for the fiscal year ended Aug. 31, 2009.
Position: Study Builder/Study ProgrammerQualification: Any Graduates Preferabaly Life Science BackgroundDesirable: 1 to 4 years experienceJob Description
  • Maintenance of Case Report Forms, Database (Oracle Clinical) objects,
  • Libraries of standard modules and objects, data mapping and transfer to an Internal reporting and analysis data repository (eDAD).
  • Electronic edit checks and data review reports using Integrated Review.
  • Provide user support, troubleshooting and maintenance of the tools and documentation related to these activities.
  • Assembly in Quark software of paper CRF booklets from libraries of objects and/or objects created by the Client Central Group, Quality testing of paper CRF modules.
  • Assembly of Oracle Clinical databases from standard or pre-built objects,
  • Creation of both internal and FDA annotations of CRFs,
  • Quality testing of Oracle Clinical database objects.
Interested Candidates Can send their resume to chandrani.x.ghosh@accenture.com


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100 positions vacant for Executive-Coding @ Dell Perot Systems, Chennai & Coimbatore

At Perot Systems, we provide solutions that support global corporations helping them achieve business-building results. Perot Systems is a Fortune 1000 corporation with over 23,000 associates across 135 locations and revenues of $2.6 billion in 2007. Our Insurance and Business Process Solutions team, based in Chennai, Coimbatore and Manila, is a leader in providing BPO services to some of the leading healthcare administrative service providers, insurance companies, financial services corporations and other Fortune 500 organizations. Dedicated to the highest standards of quality, we provide thorough training and continuous professional development opportunities to prepare our associates for rewarding assignments and exciting career.
Position: Executive - CodingQualification: M.Sc (Bio Medical Science , Bio-Chemistry, Biology, Biotechnology, Botany, Chemistry, Environmental science, Home Science, Life Sciences, Micro Biology, Nursing, Nutrition, Zoology)Job Description
  • Maintain a working knowledge of CPT and ICD-9 coding principles, governmental regulations, protocols and third party requirements regarding billing and billing documentation
  • Assure that all services documented in the patient's chart are coded with appropriate CPT-4 and ICD-9 codes. When services are not documented appropriately, seek to attain proper documentation in a timely manner
  • Achieve and maintain a high level of accuracy in professional fee coding while maintaining a high level of productivity. Accuracy will be monitored by periodic reviews by Manager
  • Conduct a review of patient hospital charts to insure compliance with coding and documentation guidelines and governmental requirements Provide written reports to Manager with results of these audits
  • Maintain a working knowledge of required billing system, the registration process and charge entry
Interested Candidates can send their resume to v_palanisamy@dell.com

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Andrew Dalke's Slides for Introduction to Python


I came across a nice set of slides from a course that Andrew Dalke taught a few years ago. They give a great introduction to Python for people interested in Bioinformatics. Here is a link (scroll to the very bottom of the page).

Andrew has a
blog, and a company with a presence on the web (where the slides are hosted), and he's on Stack Overflow as dalke.

Thanks, Andrew.



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B.Tech/M.Sc/M.Tech's can apply for Scientist Post @ Biocon, Bangalore

Biocon is an integrated biotechnology enterprise focused on the development of biopharmaceuticals. With successful initiatives in drug discovery and development, bioprocessing and global marketing, we deliver products and solutions to partners and customers in over 50 countries. We are confident that we have the defining science, world class capabilities and a focused vision to deliver the promise of new medicine to a waiting world. Today, Biocon together with group companies employs more than 2500 employees with approxmimately Rs 1,000 crore turnover and is expected to grow further during the current financial year.

Position: Scientist
Qualification: B.Tech/B.E. - Bio-Chemistry/Bio-Technology / M.Sc - Any Specialization,M.Tech - Any Specialization, Bio-Chemistry/Bio-Technology

Job Description
1) Process development and optimization for biopharmaceutical proteins produced using mammalian cells.
2) Work will include optimizing media, nutrients and process conditions for improving cell growth, productivity and quality of proteins expressed using flasks, lab bioreactors and analytical equipments like HPLCs
3) Scale-up of the processes from lab to pilot and manufacturing scale.
4) Coordinating activities between various groups of R&D, Quality and manufacturing

Desirable
1) Excellent consistent academic performance and in depth theoretical knowledge of fundamentals in the subject.
2) Good analytical skills and troubleshooting ability

Interested Candidates can send their application to careers@biocon.com


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Multiple Posts vacant at CIFA, Orissa | B.Sc/M.Sc's can walk in for interview

Applications are invited for the post of Walk-In-Interview for the following posts under the National Fisheries Development Board funded project named " Quality seed production and stock up gradation of carps through use of cryopreservation technology in the selected hatcheries of India ”

Position: Junior Research Fellow
Qualification: M.Sc Biotechnology
Desirable: 1 year work experience.
Age limit: 30 years for men and 35 years for women as on the date of interview. Relaxation will be applicable to the SC/ST/OBC and PH candidates as per rule.
Date Of Interview: 15. Jan. 2010(Saturday) at 1100 Hrs. at CIFA, Kausalyaganga, Bhubaneswar. Candidates are requested to report by 1000 Hrs. for verification etc.
Salary: Rs.10, 000/-


Position: Field Assistant
Qualification: B.Sc Biotechnology
Desirable: 1 year work experience.
Age limit: 30 years for men and 35 years for women as on the date of interview. Relaxation will be applicable to the SC/ST/OBC and PH candidates as per rule.
Date Of Interview: 16. Jan. 2010 (Saturday) at 1100 Hrs. at CIFA, Kausalyaganga, Bhubaneswar. Candidates are requested to report by 1000 Hrs. for verification etc.
Salary: Rs.6,000/-

Interested candidates should bring 5 sets of Bio-data along with two passport size photographs and one set of attested copies of all the certificates/mark-sheets/experience certificate. The proof of age to be produced at the time of interview. Original Certificates may be produced for verification. No TA/DA will be paid for attending the interview. The interested candidates may visit in our website:http://www.cifa.in for details

View Original Notification


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Bioeconomy: A Introduction

Bioeconomy refers to all economic activity derived from scientific and research activity focused on understanding mechanisms and processes at the genetic and molecular levels and its application to industrial process. It is often use interchangeably with biotechonomy.
The term is widely used by regional development agencies, international organizations, biotechnology companies. It is closely linked to the evolution of the biotechnology industry. The ability to study, understand and manipulate genetic material has been possible due to scientific breakthroughs and technological progress.
The evolution of the biotechnology industry and its application to agriculture, health, chemical or energy industries is a classic example of bioeconomic activity.

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UC San Diego Undergraduates Forge New Area of Bioinformatics


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Data Analysis Using R Functions As Objects


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What Is the HapMap?

What Is the HapMap?

This is an article that recently appeared on The International HapMap project,
http://www.hapmap.org/.

The HapMap is a catalog of common genetic variants that occur in human beings. It describes what these variants are, where they occur in our DNA, and how they are distributed among people within populations and among populations in different parts of the world. The International HapMap Project is not using the information in the HapMap to establish connections between particular genetic variants and diseases. Rather, the Project is designed to provide information that other researchers can use to link genetic variants to the risk for specific illnesses, which will lead to new methods of preventing, diagnosing, and treating disease.
Figure 1: When DNA sequences on a part of chromosome 7 from two random individuals are compared, two single nucleotide polymorphisms (SNPs) occur in about 2,200 nucleotides.
The DNA in our cells contains long chains of four chemical building blocks -- adenine, thymine, cytosine, and guanine, abbreviated A, T, C, and G. More than 6 billion of these chemical bases, strung together in 23 pairs of chromosomes, exist in a human cell. (See
http://www.dnaftb.org/dnaftb/ for basic information about genetics.) These genetic sequences contain information that influences our physical traits, our likelihood of suffering from disease, and the responses of our bodies to substances that we encounter in the environment.
The genetic sequences of different people are remarkably similar. When the chromosomes of two humans are compared, their DNA sequences can be identical for hundreds of bases. But at about one in every 1,200 bases, on average, the sequences will differ (Figure 1). One person might have an A at that location, while another person has a G, or a person might have extra bases at a given location or a missing segment of DNA. Each distinct "spelling" of a chromosomal region is called an allele, and a collection of alleles in a person's chromosomes is known as a genotype.

Differences in individual bases are by far the most common type of genetic variation. These genetic differences are known as single nucleotide polymorphisms, or SNPs (pronounced "snips"). By identifying most of the approximately 10 million SNPs estimated to occur commonly in the human genome, the International HapMap Project is identifying the basis for a large fraction of the genetic diversity in the human species.

For geneticists, SNPs act as markers to locate genes in DNA sequences. Say that a spelling change in a gene increases the risk of suffering from high blood pressure, but researchers do not know where in our chromosomes that gene is located. They could compare the SNPs in people who have high blood pressure with the SNPs of people who do not. If a particular SNP is more common among people with hypertension, that SNP could be used as a pointer to locate and identify the gene involved in the disease.

However, testing all of the 10 million common SNPs in a person's chromosomes would be extremely expensive. The development of the HapMap will enable geneticists to take advantage of how SNPs and other genetic variants are organized on chromosomes. Genetic variants that are near each other tend to be inherited together. For example, all of the people who have an A rather than a G at a particular location in a chromosome can have identical genetic variants at other SNPs in the chromosomal region surrounding the A. These regions of linked variants are known as haplotypes (Figure 2).

In many parts of our chromosomes, just a handful of haplotypes are found in humans. [
See The Origins of Haplotypes.] In a given population, 55 percent of people may have one version of a haplotype, 30 percent may have another, 8 percent may have a third, and the rest may have a variety of less common haplotypes. The International HapMap Project is identifying these common haplotypes in four populations from different parts of the world. It also is identifying "tag" SNPs that uniquely identify these haplotypes. By testing an individual's tag SNPs (a process known as genotyping), researchers will be able to identify the collection of haplotypes in a person's DNA. The number of tag SNPs that contain most of the information about the patterns of genetic variation is estimated to be about 300,000 to 600,000, which is far fewer than the 10 million common SNPs.

Once the information on tag SNPs from the HapMap is available, researchers will be able to use them to locate genes involved in medically important traits. Consider the researcher trying to find genetic variants associated with high blood pressure. Instead of determining the identity of all SNPs in a person's DNA, the researcher would genotype a much smaller number of tag SNPs to determine the collection of haplotypes present in each subject. The researcher could focus on specific candidate genes that may be associated with a disease, or even look across the entire genome to find chromosomal regions that may be associated with a disease. If people with high blood pressure tend to share a particular haplotype, variants contributing to the disease might be somewhere within or near that haplotype.

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BioXseed India Launches Biotech Finishing School

Certified Advanced Program in Genomics and Proteomics


bioxseeed-genomicsThe program aims at providing to students a best in class finishing school that would help them enhance employability and offer a pedestal to reach out to the industry.

Aristogene Biosciences is known in the industry for most authentic and practical training in the field of Biosciences. It has a well equipped 8000 sq.ft lab with the required infrastructure to support Research & Training activities. Aristogene also has an
independent R & D and process development wing, which is involved in the development of many products.

BioXseed is the Life Sciences wing of 64 Squares Consulting, a leading HR Services company with various top notch clients.

Course Content:

  • Tools in Genetic Engineering & Microbiology- Pure culture techniques, Working with phages, Cloning fundamentals, PCR
  • Cloning & Expression of Gene and Bioinformatics -Know how of complete cloning process, Important Bioinformatics tools, Knowledge ofvector host systems, DNA manipulation techniques, Expression and analysis of clones
  • Immunotechnology- Immunoprecipitaion and Agglutination techniques, Use of immunotechniques in diagnosis, ELISA, Blotting techniques
  • Protein Purification Techniques-Various chromatography techniques, Protein analysis by SDS-PAGE and western blotting, Enzymology.
  • Polymerase chain reaction & Hybridization techniques-A strong foundation for PCR based experiments - Gene amplification, RAPD analysis and related experiments, PCR - RFLP and related experiments, Southern hybridization.
  • Tools and techniques for success at workplace - Acquire the skills required for your all-round effectiveness like

o Understanding corporate environment,
o Getting your strengths noticed,
o Creative problem solving skills
o Business Etiquettes and personal grooming and the like.

Faculty for the Program:

  • Sudha with 19 years of experience specializing in Protein and nucleic acid purification, process improvement, product development, Phages, Plasmids, Restriction enzymes, and recombinant technology, and cancer cell biology.
  • Vasudha with 20 years of experience specializing in Cloning and Expression of restriction and modifying enzymes
  • Dr CR Subhashini with 15 years of experience specializing in Molecular Diagnostics & Immunology.
  • Ruskinn D with 11 years of experience specializing in Microbiology, Manufacturing & Instrumentation.
  • Shuchi Shukla with 9 years Corporate HR experience in high-end niche technology sectors.
  • Visiting Faculty from Industry.

Unique Features of this Advanced Program in Genomics and Proteomics:

  • Unique opportunity to enhance employability.
  • Advanced course that matches industry requirements with contents generally not covered in regular courses at college.
  • Student-Industry-Academia Interface. Industry Leaders will be invited to share real life experience with students.
  • A strong emphasis on hands-on laboratory training.
  • Training under the guidance of scientists with more than two decades of industry experience.
  • Proven track record in Industry Integration Program.
  • Limited enrollments with an individualized industrial learning environment.
  • Counseling services to students.
  • Curriculum and experienced speakers carefully selected to emphasize practical approaches.
  • Special Placement assistance program including Resume writing, Interview tips, Mock Interviews etc

Key Dates for the Program:

Travel & accommodation assistance can be provided for outstation students.

For more information Please fill out this Contact form or email at info@bioxseedindia.com ; shuchi@64sqs.com ; lifesc@64sqs.com Or
Call at
+91-9845215711 (Bangalore)/ +91-9953100729 (Delhi).

Download Application Form

Download Information Brochure

Apply Online


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