Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_

Enjoy the code and research work.

http://code.ohloh.net/search?s=bioinformatics

Address of the bookmark: http://code.ohloh.net/search?s=bioinformatics

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

We currently access an unprecedented knowledge on the basic components making up living systems. An ever growing number of new technologies are being developed with the capacity to systematically measure the behaviour of multiple cellular components, such as biochemical activities, biophysical properties, subcellular localization and interaction. These technologies produce large amounts of raw data that can be transformed into information by software and tools developed both in academia and industry. However, this biological information does not equal biological knowledge. As biology becomes large-scale, new methods have to be developed to integrate, visualize and query the large amounts of information available. This is usually beyond the expertise of experimental labs. The goal of this young computational systems biology group is to generate biological sense from the growing amount of biological data becoming available and turn biological information into biological knowledge. http://www.biw.kuleuven.be/m2s/cmpg/research/CSB

We seek a PhD student who will work as a computational biologist in the interdisciplinary project NATAR. Understanding the relationship between an organism’s genotype and phenotype remains one of biology’s fundamental challenges. In the project two model organisms, budding yeast and E. coli, will be exploited to better understand two complex genetic traits: ethanol and high temperature tolerance. For both organisms both natural variation and the outcomes of experimental evolution will be correlated with phenotypes. The first challenge in the project will be to identify which of the many variants in these genomes have functional effects. Then we will try to facilitate unravelling complex interactions between alleles, for example through functional gene networks that are based on a combination of published data. An important part of the generated data that underlies this project consists of high-throughput sequencing of DNA and mRNA of populations and isolates. For answering specific questions data integration with other data sources will be needed as well as the application of specific machine learning techniques. Basic molecular biology knowledge and basic programming skills are a prerequisite for this position. Experience with high throughput sequencing analysis methods, machine learning, protein interaction databases, perl/python scripting or BioconductoR are preferred. For more information contact prof. Rob Jelier (r.jelier@gmail.com) or prof. Vera van Noort (vera.vannoort@gmail.com). In your application please include a CV describing coursework, grades and previous research experience as well as a minimum of two letters of recommendation.

Starting date: from 1st of October 2013

Several sessions and workshops will be held within five focus groups, and one common theme: mountain research.

The summer school will take place in Obergurgl, in the middle of the Austrian Alps, September 5-9.

Abstract submission is now open, until February 16th: https://www.imc2022.info/summerschool/

The summer school takes place in the context of the International Mountain Conference 2022, Innsbruck, Austria: https://www.imc2022.info/

Please feel free to spread the word among potentially interested colleagues and PhD students.

"Capponi, Lisa"

More at https://evoldir.net/brian/evoldir/PostDocs//UniFreiburg_Germany.EvolutionaryTheory

Most people who have a balanced translocation have the right amount of chromosome material but it has been rearranged in some way. This may happen if two chromosomes swap pieces (a reciprocal translocation). In other cases two whole chromosomes may become stuck together (a Robertsonian translocation). This page describes what happens when someone has a reciprocal translocation.

Reciprocal chromosomal translocations occur following double-strand breaks (DSBs) in DNA when a section of one chromosome is exchanged with that of another, non-homologous chromosome. These exchanges may produce a dysfunctional fusion gene that disrupts cell growth and survival pathways, such as the translocations seen in leukemia and childhood sarcomas.

Chromosomal translocations have been well studied in cancer cell lines which are associated with two types of cancer, acute myeloid leukemia and Ewing's sarcoma, but determining how they contribute to cancer development is complicated by additional mutations and altered gene expression profiles in these cultured cells. Now, Juan Carlos Ramirez, head of the Viral Vector Facility at the Fundacion Centro Nacional de Investigaciones Cardiovasculares (CNIC) and his colleagues Raul Torres at CNIC and Sandra Rodriguez-Peralez at the Spanish National Cancer Center (CNIO) in Madrid, Spain have used a new genome editing tool, CRISPR-Cas9, to induce chromosomal translocations for the first time in a human cell line and in primary cells. The study's authors conclude by stating that the use of this technology will allow for the clarification of how and why chromosomal translocation occurs, which without doubt will allow new anti-cancer therapeutic strategies to be tackled.

Using RNA-Guided Endonuclease (RGEN) technology or CRISPR/Cas9 genome engineering technology, CNIO and CNIC researchers have shown that it is possible to obtain such chromosomal translocations. The CRISPR-Cas9 system is extremely simple to introduce a cut at the desired locus, easier to design, and cheaper than many other systems. Using the CRISPR-Cas9 system, Ramirez and his colleagues reproduced the translocations observed in Ewing’s Sarcoma (ES) and Acute Myeloid Leukemia (AML) patient cell lines in HEK293 cells and also generated the ES translocation in human mesenchymal stem cells and the AML translocation in umbilical cord blood cells.

By focusing on chromosomal translocation without the confounding characteristics of established cell lines, these new cells lines should help answer the fundamental question of what causes a cell to become cancerous. Ramirez and his team now look forward to modeling other chromosome translocations in a variety of cell types.

Reference:

http://en.wikipedia.org/wiki/Chromosomal_translocation

http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html

a) M.Sc/or equivalent in biological sciences/related areas [Position Code: PA_JRF_PF_a]
b) B.E/B.Tech/ M.Sc in biotechnology/bioinformatics/computer science/Chemistry/Physics or MCA [Position Code: PA_JRF_PF_b]
c) M.Sc/or equivalent in wildlife sciences/ecology/environmental sciences or MBBS/BVSc/MVSc. [Position Code: PA_JRF_PF_c]

(Candidates with result awaited are NOT eligible to apply)

Upper Age limit 28years

Rs.12000 / Rs.16000 (as sanctioned by the funding agency)

2. Post Doctoral Fellow/Research Associate in multiple research areas [PDF_RA]

Ph.D. (submitted/awarded) in any branch of biological Sciences. Candidates with Ph.D. in other sciences are also encouraged to apply.

Experience in molecular biology, biochemistry, structural biology, cell biology, infectious disease, conservation genetics, veterinary science, reproductive biology, and molecular diagnostics is desired but not mandatory.

[Position Code: PDF_RA]

UpperAge limit 35years

Rs. 22000- 26000 (as sanctioned by the funding agency)

3. Post Doctoral Scientist Fellow [PDSF]

Ph.D in any of the following areas: bioinformatics, next generation sequencing, high throughput data analysis, proteomics, bio-statistics, computer science, information technology, computer hardware and networking/clustering, parallel processing.
[Position Code: PDSF]

Upper Age limit 40 years

Rs. 40000 consolidated (as sanctioned by the funding agency)

Download Application: Last date for apply online: 09th Oct 2014

Advertisement: www.ccmb.res.in//index.php?view=notifications&mid=0&id=71&nid=38

Apply online http://www.ccmb.res.in/positions/temp_notif/online_form.html

More at http://www.ccmb.res.in//index.php?view=notifications&mid=0&id=71&nid=38

ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.

More http://www.arraygen.com/