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.

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

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

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.

UC San Diego Undergraduates Forge New Area of Bioinformatics

Data Analysis Using R Functions As Objects

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. (Seehttp://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.

BioXseed India Launches Biotech Finishing School

Certified Advanced Program in Genomics and Proteomics

The 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

ICMR to launch low-cost swine flu diagnostic kit

A low-cost diagnostic tool kit that can detect the swine flu virus in just five minutes is being developed by the Indian Council for Medical Research, a top official has said

The tool based on polynial chain reaction method is a simple kit to detect the virus that has so far claimed over 700 lives across the country. It will be released in a month or two, Deputy Director General of ICMR M Rajamani said here.

"It is a simple kit and can detect the virus in five minutes. It can be sent to villages for spot tests also," he told reporters yesterday.

The price would range from Rs 1,800 to Rs 2,000 while the existing imported ones cost Rs 7,000, Rajamani, who was here to participate in a conference of Medical Anthropology, said.

Join Accenture as a Clinical Data Manager | UG/PG's can send E - Resume

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. Its home page is www.accenture.com.

Position: Clinical data manager
Qualification:B.Tech/M.Sc/M.Tech Life Science graduates with 3 to 7 years experience in Clinical data management.
Desirable

Certification in one or more database management tools.
Prior experiences of interpreting edit checks/Validations in clinical data management.
Prior experience in creating clinical reports.
Knowledge of Business objects, to build report. And understanding the limitations of the tool to build reports.
Knowledge of SQL Developer.
In depth knowledge of Clinical Data management.
Knowing Responsibilities of each role involved in Clinical Trials Management.
Good knowledge of office tools – MS Word and MS Excel.
Good communication skills.
Analytical and Reasoning skills.
Has worked as a project lead in any of the processes.