bioinformatics,naveenbioinformatics

APPLICATIONS AND DATA ANALYSIS:

[fquote]NGS 2016 Glasgow, the 3rd annual Next Generation Sequencing conference to take place in Scotland will be held on 27th & 28th April 2016 at the IET Teacher building in the heart of Glasgow city centre.  This event is held in partnership with NHS West of Scotland Genetics Service and the University of Glasgow’s Polyomics research facility.  In conjunction with the conference there will be a one day workshop on 26th April that will provide Next Generation Sequencing data analysis training to those working in the wetlab who want to be able to analyse the data and understand the data analysis workflows.[/fquote]

[tab] [content title="When"]CONFERENCE ON 27TH & 28TH APRIL WORKSHOP ON 26TH APRIL[/content] [content title="Where"]IET TEACHER BUILDING, GLASGOW [/content] [content title="SPEAKERS"]Prof Dame Janet Thornton, EMBL-EBI Prof Sir John Burn, International Centre for Life[/content] [content title="REGISTRATION"]https://biotexcel.com/event/ngs-2016-glasgow/#tab4[/content] [/tab]
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naveenbioinformatics,bioinformatics

, - Ref:1533306  @ University College London (UCL)

[fquote] We are looking for a postdoctoral researcher to work on a Wellcome Trust funded project in Professor Claudio Stern's research group. The project involves work on the molecular mechanisms that control embryonic axis formation and twinning including identifying genes involved in twinning in humans. The post also offers opportunities to develop new computational tools for bioinformatics and/or modelling and to publish these as methodological papers when appropriate.[/fquote]

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@ University of Texas Health Science Center

[fquote]This position of bioinformatics faculty with a primary appointment in the Department of Epidemiology and Biostatistics (DEB) at the University of Texas Health Science Center at San Antonio (UTHSCSA) School of Medicine, will have overall responsibility for strengthening our collaborative research and direct a competitive bioinformatics service program. The candidate will apply bioinformatics techniques to analyze the next-generation sequencing, microarrays and other high-throughput profiling data to gain insights into the biology of diverse organisms with an emphasis on cancer research. Candidate will also manage a service component of our next-generation sequencing facility. The bioinformatics faculty will promote the development of interdisciplinary bioinformatics research in translational, clinical and community settings, and provide oversight and guidance to research staff and post-graduate student to conduct independent research.[/fquote]

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 @ Harvard Medical School

[fquote]This is an exciting opportunity to join a growing group at the Harvard Medical School (HMS) and have a major impact on the way information technology is delivered and research is done in a world class research institution. HMS Research Computing is the principal provider of High Performance Computing (HPC) services to the research community at Harvard Medical School. The group supports a cluster - with thousands of processor cores, terabytes of memory and petabytes of storage - and enables access to hundreds of applications for computational biology. The successful candidate will be an integral member of the team and a contributor in building computational services in support of the research community.[/fquote]
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on Translational Bioinformatics

[fquote]The conference will be relevant for researchers and other actors with interest across the domains of bioinformatics, systems biology, chemoinformatics, medical informatics, biology and medicine.The Conference is organized by the “Novo Nordisk Foundation Center for Protein Research” at the University of Copenhagen and supported by the Horizon 2020 MedBioinformatics project. MedBioinformatics aims to develop bioinformatics tools and applications of relevance for analysing the huge amount of data and knowledge generated in healthcare and biomedical research with the further aim of facilitating translational research and precision medicine.[/fquote]
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 for Genome Assembly

naveenbioinformatics,bioinformatics

















[fquote]String and de Bruijn graphs are two graph models used by most genome assemblers. At present, none of the existing assemblers clearly outperforms the others across all datasets. We found that although a string graph can make use of entire reads for resolving repeats, de Bruijn graphs can naturally assemble through regions that are error-prone due to sequencing bias.[/fquote]

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through social media

[fquote]Social media is no doubt a powerful force when it comes to the sharing of information and ideas. The problem is that not every article shared on Facebook or Twitter is true. Misinformation, conspiracy theories and rumours abound on the Internet, helping to propagate and support sentiments such as climate doubt and other forms of environmental and scientific skepticism.[/fquote]
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[fquote]This website is dedicated to the researchers in the field of molecular biology. It harbors several useful links to bioinformatics online tools and software.The universal resource locator of these websites usually changes due to several reasons. It is a Herculean task and really difficult to track the changes every time by a single person. The web-links can be maintained up to date only by collaborative help of the researchers by furnishing information regarding the change in web-site address.[/fquote]

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in the Fourth Industrial Revolution

[fquote]Five years from now, over one-third of skills (35%) that are considered important in today’s workforce will have changed.By 2020, the Fourth Industrial Revolution will have brought us advanced robotics and autonomous transport, artificial intelligence and machine learning, advanced materials, biotechnology and genomics.[/fquote]
  • These developments will transform the way we live, and the way we work. Some jobs will disappear, others will grow and jobs that don’t even exist today will become commonplace. What is certain is that the future workforce will need to align its skillset to keep pace.
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navenbioinformatics,bioinformatics

















Design at the intersection of technology and biology

[fquote] Designer and architect Neri Oxman is leading the search for ways in which digital fabrication technologies can interact with the biological world. Working at the intersection of computational design, additive manufacturing, materials engineering and synthetic biology, her lab is pioneering a new age of symbiosis between microorganisms, our bodies, our products and even our buildings.[/fquote]
  • TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes (or less). 

@ fragnet consortium

Recruitment

[fquote]We are looking for 15 highly motivated and talented students with an MSc degree who are interested in an ambitious multidisciplinary project on Fragment-Based Lead Discovery (FBLD).The objectives of FragNet are to (a) train a cohort of ESRs across FBLD methods and (b) develop individual skills in research into either new methods in FBLD or to apply FBLD to interrogate biological systems.At this moment we have 15 vacancies (see Projects)[/fquote]

Application procedure deadline February 12th, 2016:

1. Send your application mentioning the ESR number in the subject line to [email protected]
2. Please send all the necessary information as one pdf file to [email protected]


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WITHIN THE HEALTH SYSTEM

naveenbioinformatics














We live in a society that is able to generate massive amounts of data in seconds. In fact, it has been estimated that in two days we generate as much data as we did since the birth of civilization to the completion of the Human Genome Project in 2003. The health system is no exception in the age of large data, now that the available data come from a variety of sources, such as electronic health records, laboratories, medical imaging systems and medical notes. 
  • Extracting the valuable information all this data contained in the health system will help increase biomedical knowledge so we can advance towards a personalized, participatory, predictive and preventive medicine. 

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naveenbioinformatics,bioinformatics

Could Be a Big Win for Bioinformatics

The National Biotechnology Development Strategy makes a lot of the right noises. However, at this point, it is silent on how its programmes will be implemented.
  • The Department of Biotechnology (DBT) of the Government of India announced a National Biotechnology Development Strategy (NBDS), covering the period 2015-2020, on December 30, 2015. The overarching goal of NBDS is to set in place processes that will result in the growth of the Indian biotechnology sector into a $100 billion industry by the year 2020. 

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naveenbioinformatics,bioinformatics

Ashkan Fardost "A Cure for No Cures - The Next Generation of Medicine" at TEDxBerlin Ashkan received his PhD in pharmaceutical chemistry from Uppsala University. He’s been a member of the scientific community since 2009, with several peer-reviewed publications in acclaimed scientific journals.


  • Before his scientific ventures, in the mid 90’s, he leveraged computers, the early internet, and the art of growth hacking, to acquire a record deal and launch an international music career as a 17-year old.
  • He has always been fascinated by the exponential progress of technology and how it empowers and transforms our lives, cultures and societies.
  • Today, Ashkan is a public speaker and consultant for tech startups in Stockholm. He also appears on Swedish national television as a science reporter.

Italy is the latest country to sign the ELIXIR Consortium Agreement and join ELIXIR as Member, following the ELIXIR Board’s approval of Italy's application.

  • The ELIXIR Node in Italy is organised as a Joint Research Unit, coordinated by the National Research Council (CNR). It brings together 13 partners, including seven Italian universities and four High Performance Computing (HPC) centres.
  • The Italian bioinformatics community has a strong track record in human, animal and plant genomics and has been involved in several genome projects (for example the Sardinians genome project, the domestic horse and the grape and peach genomes). Other areas of focus for the Node include metagenomics, epigenomics, proteomics and bioinformatics training. ELIXIR will in turn also benefit from the experience and expertise of Italy's four High Performance Computing centres in managing HPC services in various scientific fields.

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The performance of the MinION™ miniature DNA sequencing device has been evaluated by an open, international consortium, and the resulting recommendations and protocols published before peer-review on the F1000Research platform.
  • The MinION, a handheld DNA-sequencing device developed by Oxford Nanopore, has been tested and evaluated by an independent, international consortium coordinated by EMBL-EBI. The innovative device opens up new possibilities for using sequencing technology in the field, for example in tracking disease outbreaks, testing packaged food or the trafficking of protected species.

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FDA starts beta-testing 'the most advanced bioinformatics platform in the world'
The FDA has started testing the precisionFDA platform it developed with DNAnexus. The closed beta test phase is the precursor to a more widespread rollout of the system, which the CEO of DNAnexus has described as being "the most advanced bioinformatics platform in the world."

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[accordion] [item title="#1:PhD scholarships in the life sciences 2016 @ IMPRS"]The special feature of our 3-year PhD program is its emphasis on interdisciplinary interactions. We want to train the next generation of scientists to study complex biological processes that cannot be adequately understood within the limits of a single discipline. Traditionally separate fields covered include: Biophysics,Structural, molecular and cellular biology,Biochemistry and genetics,Bioinformatics, genomics and proteomics Evolutionary biology Read More[/item] [item title="#2:PhD Students in Molecular Medicine @ DANDRITE"]The Nordic EMBL Partnership for Molecular Medicine, which includes the Danish Research Institute for Translational Neuroscience (DANDRITE, www.dandrite.au.dk), Institute for Molecular Medicine Finland (FIMM, www.fimm.fi), Laboratory for Molecular Infection Medicine Sweden (MIMS, www.mims.umu.se), and Centre for Molecular Medicine Norway (NCMM, www.ncmm.uio.no) is dedicated to research excellence in molecular medicine, life science research that investigates the molecular basis of disease and explores molecular and genetic based treatments. Read More[/item] [item title="#3:October 2016 - PhD studentship @ The MRC-PHE "]The MRC-PHE Centre for Environment and Health is an internationally recognised centre of excellence for leading cutting edge multidisciplinary research on the health effects of environmental pollutants and the translation of this knowledge to inform national and international policies to improve health. ​We are uniquely placed to collaborate with expert research groups nationally and internationally to produce high quality cutting edge research and work with public health agencies to apply the results to improve population health. A key component of our Centre’s strategic aim and mission is to train and develop the next generation of research and policy leaders in the environment and health arena.Read More[/item] [item title="#4:15 International PhD Positions @ fragnet consortium"]We are looking for 15 highly motivated and talented students with a MSc degree who are interested in an ambitious multidisciplinary project on Fragment-Based Lead Discovery (FBLD). The objectives of FragNet are to (a) train a cohort of ESRs across FBLD methods and (b) develop individual skills in research into either new methods in FBLD or to apply FBLD to interrogate biological systems. Read More [/item] [/accordion]

naveenbioinformtics,bioinformatics
The dream of melding biological and man-made machinery is now a little more real with the announcement that Columbia Engineering researchers have successfully harnessed a chemical energy-producing biological process to power a solid state CMOS integrated circuit.

According to study lead professor Ken Shepard, this is the world's first successful effort to isolate a biological process and use it to power an integrated circuit, much like the ones we use in phones and computers.
The researchers developed the system by using an artificially created lipid bilayer membrane containing naturally occurring ion pumps, which are powered by the biological world's "energy currency molecule," ATP (adenosine triphosphate). ATP is the coenzyme that transfers chemical energy between living cells. It is an end product of processes such as photosynthesis and cellular respiration, and it powers the mechanical work of living systems such as cell division and muscle contraction.

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The world’s most popular online course is a general introduction to the art of learning, taught jointly by an educator and a neuroscientist. “Learning How To Learn,” which was created by Barbara Oakley, an electrical engineer, and Terry Sejnowski, a neuroscientist, has been ranked as the leading class by enrolment in a survey of the 50 largest online courses released earlier this month by the Online Course Report website.

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naveenbioinformatics,bioinformatics











Children suffering from mystery illnesses have been diagnosed with genetic diseases for the first time after taking part in the government’s 100,000 Genomes project.
  • In August 2014, David Cameron announced a landmark scheme to map the genetic codes of tens of thousands of people suffering from cancer and rare diseases, in the hope of finding out which genes were responsible.
  • Now two little girls have finally been given a diagnosis at Great Ormond Street Hospital (GOSH) after scientists found mutations in their genes which had never been seen before.

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The tardigrade genome has been sequenced, and it has the most foreign DNA of any animal
Source:http://www.sciencealert2014.com/the-tardigrade-genome- 
  • Scientists have sequenced the entire genome of the tardigrade, AKA the water bear, for the first time. And their results suggest that this weird little creature has the most foreign genes of any animal studied so far – or to put it another way, roughly one-sixth of the tardigrade's genome was stolen from other species. We have to admit, we're kinda not surprised. 

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High Throughput Glycan Characterization




Keeley Murphy, Senior Life Sciences Mass Spectrometry Marketing Specialist, describes the development of bioinformatics support for high throughput isomeric separation and the structural identification of glycans by LC-MS.










2015 has been another stellar year for BMC Bioinformatics. Here we look back at five of the articles published this year that have drawn the most attention from our readers.

  • One of our devoted Section Editors highlighted an issue that is highly relevant in these times of increasing attention to reproducibility and development of open data policies – how should we handle the growing amount of supplementary information, which in many cases can surpass the length of the main text several fold? Supplementary material is necessary for a complete scientific record, especially in articles governed by size limitations. However, improperly implemented, such files might both obstruct thorough peer-review, reuse of data, and fair recognition of previous work through citation tracking.

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EuPathDB Parasite Genomics Workshop
Walter Eliza Hall Institute of Medical Research
Melbourne, Australia
February 15-19, 2016
Application deadline: January 15, 2016

This workshop will focus on providing attendees with thorough hands-on training in genomic scale data analysis based on parasite genomic resources.  Attendees should expect to become adept at using databases such as PlasmoDB, ToxoDB and TriTrypDB to support their basic research.  Topics to be covered include:
  • Genome browsing and comparative genomics
  • Formulating complex biological queries in computationally accessible form
  • Integrating functional genomics data (microarrays, proteomics, etc) with genome sequence data
  • Theoretical aspects of genome re-sequencing
  • Querying genetic diversity on a genome-wide scale
  • Metabolic pathways and pathway analysis
  • Working with next-generation sequence data (mapping, variant calling, etc)

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  • R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R provides a wide variety of statistical and graphical techniques, and is highly extensible.One of R’s strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. R is an open source alternative to SAS. That way R is highly matured and better than SAS for all needs of numerical analysis and other quantitative techniques. R is free and can be obtained from https://www.r-project.org. This video deals with gene sequence analysis.

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein.
A Beginner's Guide to RNA-Seq Data Analysis Course


  • All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

When?

  • 1 - 5 February 2016

Where?

  • Leipzig, Germany

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What is APBC?

The Asia Pacific Bioinformatics Conference (APBC)
  • The Asia Pacific Bioinformatics Conference (APBC) series is an annual international forum for exploring research, development and novel applications in the field of Bioinformatics. The aim of APBC is to bring together academia and industry to share knowledge and experiences, and to showcase innovations and achievements. It has been held since 2003 around Asia Pacific Regions (please refer to the Previous Conferences section).

APBC 2016

  • APBC is holding its fourteenth annual meeting in the beautiful San Francisco Bay Area January 11-13th 2016. The conference venue South San Francisco Conference Center is conveniently located in the heart of the biotech region, minutes from San Francisco Airport and 15 minutes from downtown San Francisco. San Francisco Bay Area is in the Pacific Time Zone. 

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