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About the Network Portal

  • version: 0.0.1
  • The Network Portal is a database of gene transcription regulatory networks and enables exploration, annotation and comparative analysis. Deciphering the complexity of biological systems requires a systems-level view of regulatory players and their interactions. However, inference of these complex interactions is challenging, and further, visualizing and analyzing these interactions often requires advanced computational expertise, tools and resources. Network Portal provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis development.

Method


method
Network Portal integrates identification of conditionally co-regulated group of genes (performed using cMonkey) and inference of regulatory influences (performed using Inferelator). In addition, it is integrated with MicrobesOnline for genomic information, RegPrecise for collection of manually curated regulatory inferences, and RegPredict for Regulon Inference by Known Position Weight Matrix (PWM).
The Network Portal aims to be flexible, modular and comprehensive. Therefore we designed our framework in two interconnected layers.

  1. Automated Network Inference Pipeline: The first phase of this module leverages various data (microarray, RNAseq etc.) from validated resources (GEO, MicrobesOnline, ArrayExpress etc), checks for quality control and performs necessary optimizations to ensure compliance with ENIGMA Standards and Best Practises. The second phase of the module integrates algorithms to infer regulatory networks. Currently two algorithms (cMonkey and Inferelator) are integrated with the portal. Upcoming releases will allow developers and researchers to plugin their favorite inference algorithm seamlessly without worrying about data formats or downstream applications. In the final phase of the automated inference pipeline, processed output is transmitted to a database that can be accessed programmatically within and outside of the portal.
  2. Visualization and Analysis: This layer provides online tools for visualizing network information in the context of other available data (such as genomics, proteomics, orthology etc.) in order to help with hypothesis validation and creation. Similar to the automated Inference Pipeline, this layer is also designed to be modular and flexible. We already provide tools that highlight important connections between various types of data and network information. Developers are also encouraged to design visualization and data harvesting tools that can be plugged into our visualization framework. For example, in addition to showing regulatory influences for a particular gene, a RegPrecise plugin can leverage verified regulatory informations and integrate with network portal data. Moreover, in order to give researchers more freedom, Network Portal is integrated with Gaggle Framework which enables broadcast of data among various desktop and online tools.

Credits

images
The Network Portal was developed as part of the DOE Knowledgebase effort. While the Network Portal integrates data, algorithms, software, and technologies that have been developed by the community, development of the portal itself is being driven by efforts focusing on the biology of specific organisms including:






  1. Desulfovibrio vulgaris (funded by ENIGMA)
  2. Methanococcus maripaludis (funded by ENIGMA and DOE)
  3. Halobacterium salinarum (funded by NSF, NIH and DOE)

Tools

Tools
  • Python, Django, NetworkX, Solr, PostgeSQL, Cytoscape Web, jQuery, the R project
  • Data sources include: Microbes Online, KEGG, NCBI, GO, TIGR

Sourcecode and Database Downloads

images

License

  • This software is released under the terms of the LGPL. Copyright (C) 2011 Institute for Systems Biology

Web link

Related video

b
Bioinformatics is one of the fastest emerging interdisciplinary research areas, which may be defined as an ‘interface between biological and computational sciences’. Most of the Bioinformatics work can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. Though the US remains the largest market in the world, Asia-Pacific countries (particularly India and China) are witnessing the fastest growth and are anticipated to emerge as the dominating forces in the future.
  • The Indian bioinformatics market, which is the smallest of biotech industry segments constituting barely 2% of the market share in overall revenue, grew by 11.5% in FY 2010-11 to reach US$ 58 Million. The market is backed by factors, such as tracking of discovery activities, data analysis, and pharmaceutical research. As global players augment drug discovery and research activities, the outsourcing of bioinformatics related work will also strengthen in the same proportion. It shall also boost the Indian market that may register a CAGR of around 26% during the period FY 2012 to FY 2015.
  • The report “Indian Bioinformatics Market Forecast to 2015” has depicted a true picture of Indian bioinformatics market, its current and future position in the biotech industry and key drivers and restraints. An in-depth insight into the advantages offered by India as a country in bioinformatics has also been provided here. In such a way, clients can attain an understanding of workforce, educational structure, and government support with respect to bioinformatics in India.
b
  • The report is an outcome of an extensive research and prudent analysis of Indian bioinformatics market that seeks to deliver reliable statistics and important information associated with key aspects/areas. While forecasting the market values in key parts of the report, a valuable emphasis has been given to the usage of effective methods and techniques. The report also provides a brief description of market players actively supporting the industry developments. Overall, the report is meant to be a complete source of knowledge and analysis for clients interested in Indian bioinformatics market.

Read more

Related video

East_Carolina_university_logo

Job Description:

  • The Department of Biology at East Carolina University, Greenville, NC, the third largest campus in the University of North Carolina system, invites applications for a nine-month tenure-track position at the Assistant Professor level with research interests in Bioinformatics, to begin August 18, 2014.
  • We are looking for a broadly trained biologist with expertise in bioinformatics and computational biology.
  • The successful candidate will possess a research program with comparative or evolutionary components and have experience with large datasets, such as those generated through next-generation sequencing technologies.
  • She/he will be expected to establish a vigorous, well-funded research program, actively engage in undergraduate and graduate classroom teaching in Bioinformatics and related disciplines, mentor students in the M.S. and Ph.D. programs, and engage in university, community, and professional service.
  • Opportunities exist for collaboration within Biology as well as with other departments, including those at the Brody School of Medicine (http://www.ecu.edu/med/), and ECU's Center for Biodiversity.
  • Please visit our website at http://www.ecu.edu/biology for more information on the department.
  • Appointment at the Associate Professor or Professor level may be considered for a candidate with a well-established record of teaching and research.

Minimum Qualifications:

  • A Ph.D. in Bioinformatics, Biology or Biology-related fields with bioinformatics training and at least one year of postdoctoral research experience are required.
  • Qualifying degrees must be received from appropriately accredited institutions and conferred by the time of hire.

Special Instructions to Applicants:

  • Applicants must submit a cover letter, curriculum vitae, statements of research interests and teaching experience/philosophy online at www.jobs.ecu.edu using the position number 934040 - Tenure Track Faculty in Biology, Bioinformatics.
  • Candidates should also arrange for three current letters of reference to be e-mailed (in PDF form only, from recommender) to [email protected] Official transcript and original hard-copy reference letters are required upon employment.
  • Inquiries may be directed to Dr. Jinling Huang ([email protected]), Search Committee Chair. Review of applications will begin on December 2, 2013 and continue until the position is filled.

Date Initial Screening Begins:

  • 12-02-2013

About ECU

about_banner
  • East Carolina offers research opportunities for both undergraduate and graduate students. We seek the best and brightest minds to meet the challenges of the 21st-century, and we provide the support and assistance needed to ensure that the world's next great discovery happens here.

Related video

transcriptome

RNAseqViewer let you visualize the various data from the RNA-Seq analyzing process, for single or multiple samples. By focusing on gene expression and transcript isoforms, the program offers innovative ways to present the transcriptome data.

Program features

 

tkfoplp-05

RNAseqViewer currently supports 7 types of data often used in RNA-Seq analysis (see table 1). Different types of view for each data set allow the visualization of different levels of information, including heatmap-like views for informative and yet very compact tracks, making possible to visualize dozens of samples simultaneously.

The user interface has been design to enable smooth browsing of the data. RNAseqViewer supports dynamic zooming and panning using the mouse, the keyboard or the buttons of the interface. Direct access to a specific position is possible by specifying coordinates or a gene's name.

Special attention has been given to the memory management, so that very large data sets can be visualized without exceeding memory limits nor affecting the fluidity of the user interface.

Other features include the possibility to hide intronic regions, the choice of the interface language (currently English, Chinese or French) and the possibility to print out the graphs or to export to PDF or image format.

Download RNAseqViewer v0.8.0

 

Software-downloads

RNAseqViewer is written in Python 3 and makes use of some additional libraries. Hence you have two options to run it. The first one is to download the source code, install Python and the necessary libraries, and run the program as a Python script. The other and easier option is to download the program as an executable which includes the Python interpreter and the necessary libraries.

 

The source code and binaries are freely available for academic use.

Please read the installation guide and the illustrated quick start tutorial.

  • Windows 32bit installer (12 Mb)

    Download and run the installer to install the program.

    Tested on Windows XP pro SP3 and Windows 7 SP1.

  • Windows 64bit installer (13 Mb)

    Download and run the installer to install the program.

    Tested on Windows XP pro SP3 and Windows 7 SP1.

  • Ubuntu and openSUSE binaries (15 Mb)

    Download and uncompress the package, then run the executable "RNAseqViewer".

    Tested on Ubuntu 12.04 and openSUSE 12.2.

  • Debian binaries (16 Mb)

    Download and uncompress the package, then run the executable "RNAseqViewer".

    Tested on Debian 7.

  • You can also download some sample data for testing purpose: sample_data.tar.gz (12 Mb) or sample_data.zip (13 Mb)

Related video

_PMP3272smal

source

  • Med Tech Newswire

The expert provider of bioinformatics software and services across a wide range of life science and other sectors, has announced the final closing of a £1 million fundraising, as it continues to expand and develop new bioinformatics products. Eagle uses advanced computing to answer complex biological problems, from fighting cancer to breeding better crops.

  • This second round was led by members of London Business Angels, with further support from the Angel CoFund and first round investor, Jonathan Milner (CEO of Abcam) is addition to the £590k invested in September and brings the total raised to £1 million.
  • This has been the first time Eagle has taken investment, following five years' of profitable growth, and the money will be used to expand Eagle's current offering - including the development of ElasticAP, a SaaS (Software-as-a-Service) subscription platform, that enables customers to analyse complex genetic data through the Cloud using Eagle's expertise. The company also plans to expand its consulting business by pushing further into non-traditional areas for bioinformatics such as consumer goods, food safety and animal health.
  • To meet the growing demands of developing ElasticAP, and support the growing client base, Eagle is doubling the size of its team. The new hires will build capacity in both bioinformatics and software development.

David Flanders, CEO of Eagle said: "With the fundraising now secured, we can really begin to make progress in achieving our commercial goals. We have already begun our expansion, and the development of ElasticAP relationship is underway – all while we continue to grow the consulting side of the business."

  • George Whitehead, Chairman, Angel CoFund, said: "Eagle has been a profitable business for a number of years, but needed this cash injection to get the business to the next stage. This is exactly what the Angel CoFund is all about – identifying high growth UK tech businesses and making sure they receive the right levels of funding to have a real impact."

Anthony Clarke, London Business Angels CEO, comments: "Following completion of its £1m funding round, Eagle Genomics is now well placed to exploit its high growth potential in the exciting bio-informatics market. I am delighted that a syndicate of LBA investors led by one of our Angel Investors, including our EIS Roundtable Syndicate Fund 2013, has been able to contribute circa £200k to this funding round alongside the Angel CoFund with many of these investors being sector experts who will able to add real value to the company going forwards."

  • Eagle has over 30 customers worldwide from the large pharmaceutical, biotechnology, crop science, bio-fuels, personal hygiene, and animal health sectors.

page1-770px-PATRIC_brochure.pdf

What is PATRIC?

index

PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools.  PATRIC sharpens and hones the scope of available bacterial phylogenomic data from numerous sources specifically for the bacterial research community, in order to save biologists time and effort when conducting comparative analyses.  The freely available PATRIC platform provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses in a one-stop shop.  PATRIC is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division.

 

 

What Can I Do @ PATRIC?

Transcriptomics Data at PATRIC

question1.001

PATRIC has three primary types of experiment data, Taxonomy or Genome level, Gene or CoDing Sequence level, and Your Own Uploaded Experiment data.  Learn about these types of experiment data, where you can find them, and some of the potential analyses you can do.

 

 

 

 

Protein Family Sorter

  • Compares protein families across closely related or diverse groups of genomes, visualizes them using interactive heatmaps, and generates multiple sequence alignments and phylogenetic trees for individual families. The heatmap view is an interactive visualization tool that provides an overview of the distribution of proteins across a selected set of genomes.

Comparative Pathway Tool

  • Supports comparison of consistently annotated metabolic pathways across closely related or diverse groups of genomes and visualizes them using interactive KEGG maps and heatmaps. The heatmap view is an interactive visualization tool that provides an overview of the distribution of genomes across the set of EC numbers within a selected pathway

Genome Metadata

  • Supports searching for and locating genomes of interest based on various combinations of 61 different metadata fields. For instance, all genomes that have been isolated from humans, genomes related by phylogeny, or genomes related by lifestyle.

Show all available tools

 

Read more

New-Genome-Analysis-Reveals-Dozens-of-Cancer-Triggers

Author:

  • Dana Sparks

Source:

Mayo Clinic

A new study at Mayo Clinic is using genomic sequencing to develop customized treatments for men with castration-resistant prostate cancer, a progressive and incurable stage of prostate cancer, which no longer responds to hormone therapies that stop or slow testosterone production.

  • Oncologist and principal investigator of the Prostate Cancer Medically Optimized Genome-Enhanced Therapy (PROMOTE) study, Manish Kohli, M.D., says, “Men with  castration-resistant prostate cancer have abysmal survival rates, typically living an average of two years once hormone therapies fail." Dr. Kohli says the poor prognosis for men with this cancer highlights the need for studies like PROMOTE, which seek to match new targeted drugs with the genomic characteristics of individual patients’ tumors.

20949-004-D07FB3BA

source:

BBC

Author:

  • James Gallagher

Fellow researchers have described him as "one of the greatest scientists of any generation" and as "a real hero" of British science.

  • He is considered the "father of genomics" after pioneering methods to work out the exact sequence of the building blocks of DNA.

  • Dr Sanger also developed techniques to determine the structure of proteins.

  • He was born in 1918 in Gloucestershire and initially planned to follow his father into medicine.

  • However, he followed a career in biochemistry at the University of Cambridge.

It is impossible to exaggerate the impact of Fred Sanger's work on modern biomedical science.

Prof Colin Blakemore

Glittering success

  • He is the only Briton to win two Nobel Prizes and the only scientist to have been awarded the prize for Chemistry twice.
  • The first came in 1958 for developing techniques to work out the precise chemical structure of proteins.
  • Proteins are made up of amino-acids. Dr Sanger was able to determine which amino-acids and in what order were used to build the hormone insulin.
  • He then turned to DNA and its building blocks, bases.
  • Dr Sanger's group produced the first whole genome sequence, made up of more than 5,000 pairs of bases, in a virus.
  • He was awarded his second Nobel Prize in 1980 for developing "Sanger sequencing" - a technique which is still used today.

At the time he attributed his success to fellow researchers and his wife: "I was married to Margaret Joan Howe in 1940. Although not a scientist herself she has contributed more to my work than anyone else by providing a peaceful and happy home."

  • He was awarded one of Britain's highest honours - the Order of Merit - in 1986. However, he declined a knighthood as he did not want to be called a "Sir".
  • The Wellcome Trust Sanger Institute in Cambridgeshire, which specialises in the understanding of the genome, is named after him.
  • When the founding director of the institute, John Sulston, asked Dr Sanger if he was comfortable with the site being named after him, the response was: "It had better be good".

He worked until the age of 65 when he retired to spend more time gardening and "messing about in boats".

'Transformative' healthcare

  • Dr Jeremy Farrar, director of the Wellcome Trust, said: "I am deeply saddened to learn of the death of Fred Sanger, one of the greatest scientists of any generation and the only Briton to have been honoured with two Nobel Prizes.
  • "Fred can fairly be called the father of the genomic era. His work laid the foundations of humanity's ability to read and understand the genetic code, which has revolutionised biology and is today contributing to transformative improvements in healthcare."
  • Prof Colin Blakemore, the former chief executive of the UK Medical Research Council, said: "The death of a great person usually provokes hyperbole, but it is impossible to exaggerate the impact of Fred Sanger's work on modern biomedical science.

"His invention of the two critical technical advances - for sequencing proteins and nucleic acids - opened up the fields of molecular biology, genetics and genomics.

  • "He remains the only person to have won two Nobel Prizes in Chemistry - recognising his unique contribution to the modern world.
  • "Yet he was a disarmingly modest man, who once said: 'I was just a chap who messed about in his lab'.
  • "Fred Sanger was a real hero of 21st Century British science."

source:

BBC

Author:

  • James Gallagher
 

MinION_117

Author:

  • Dr. Bertalan Meskó

Source:

ScienceRoll

I’ve lived through the era of the Human Genome Project, then the Personal Genome Project, after that, the race to lower the price of genome sequencing, but what if sequencing your genome would cost nothing and you shouldn’t have to send your samples to laboratories full of sequencing machines, but you could sequence your genome at home using a USB stick.

We are not far from that.

To sequence anything longer than a few hundred base pairs, scientists mince up thousands of copies of the target DNA, sequence all the fragments, and use software to painstakingly reconstruct the order of the DNA bases by matching overlap within fragments. A new approach, called nanopore sequencing, can handle long strands of DNA at once, eliminating the need for overlap analysis. As a result, nanopore sequencers could be cheaper, faster, and more compact than other DNA sequencers. They can also accurately sequence stretches with many repeating base pairs. The MinION from Oxford Nanopore Technologies connects to a USB port. Soon, anyone with $1,000 and a computer will be able to sequence DNA.

dna

 

Author:

  • Dr. Bertalan Meskó

Source:

ScienceRoll

images

Source:

Memory specialist Micron has announced a new accelerator processor that it claims outperforms Intel's chips when it comes to dealing with streaming data.

  • The "Automata Processor" was announced by the company on Monday and billed as a device that uses the inherent parallelism of memory architectures to speed the ingestion and processing of large data sets.
  • Potential applications of the chip include genomic analysis and various security tasks such as the classification of online video footage.
  • The chip should be available in 2014 and the company has taped out the first silicon, it said.
  • Each Automata Processor uses a DDR3-like memory interface, and will be made available either as standalone, or in DIMM modules. It has an inter-chip bus, and has a power draw of around 4 watts.

  • In tests, a cluster of 48 of the processors on a PCIe board comfortably beat a 48-chip cluster of Intel Xeon 5650s when trying to complete a tough 'Planted Motif Search' problem.

The design is based on an adaption of memory architecture and exploits "the inherent bit-parallelism of traditional SDRAM," according to a Micron paper describing the technology. This sets it apart from Intel's "Xeon Phi" accelerator, which gets its number-crunching skills from an array of many, many low-power wimpy x86 chips.

  • Automata processors should comfortably beat field programmable gate arrays (FPGAs) on performance, the paper says. "We believe that our architecture also implies a new parallel programming paradigm".
  • As it is designed as an accelerator, it will need to piggyback on a typical processor, though this could take the form of a low-power ARM chip. It will also be tough to program for, though Micron says it is working with researchers to ease this issue.

Source:

BY4g3sUCcAAX60m.jpg large

About

Frontiers in Neuroscience for Young Minds is a scientific journal that includes young people (from 8 to 18) in the review of articles. This has the double benefit of bringing kids into the world of scientific research – many of them for the first time – and offering active scientists a platform for reaching out to the broadest of all publics.

  • All articles in Frontiers for Young Minds will be reviewed and approved for publication by young people themselves. Established neuroscientists will mentor these young Review Editors and help them review the manuscript and focus their queries to authors. To avoid overburdening the young Review Editors, revised manuscripts will in turn be reviewed by one of the stellar Associate Editors of Frontiers in Neuroscience for Young Minds.

How does it work?

 

New research or review articles are reported on a subject area that fits into one of the categories mentioned above. This can be work published by Frontiers or any other publisher;

The scientists write up their research for submission to the Journal, following our editorial guidelines as outlined below;

The report is handled by one of our prestigious associate editors, who will manage the process of peer review ;

Your article is reviewed by a young mind, mentored by a scientist with experience in peer review.

The young mind and mentor will require that the authors write clearly, concisely and with enthusiasm!

The articles are then validated by the Associate Editor, revised and forwarded to the Frontiers office for production;

The text is typeset and published on kids.frontiersin.org.

The identities of the reviewers (first name only for the young mind) and author are published with the article.

 

How can you get involved?

 

If you are interested in becoming a Frontiers Young Minds Reviewer, please contact our editorial office with a short biography and a letter. Is there someone among your family or friends who is a scientist and who can act as mentor for the project?

If you would like information about becoming a Young Minds mentor, please send your contact information and to our editorial office and we can explore these opportunities together.

If you are an author, send us an abstract with the reference to the original research article, or a short summary if you are planning to submit a review. In both cases, please indicate into which subject area above your contribution should be placed. You will then be contacted by an Associate Editor, who will be handling the review of your Young Minds paper. In the second half of 2014, we will open our manuscript submission and review platform to handle Young Minds papers; in the interim, please submit your materials with a cover letter to [email protected]. Once approved, we will ask you submit a two to three page article appropriate for our community of Young Minds, including two or three figures, and a very short list of references (no more than 5). Please make a special effort for the figures — these will help get you message across to the readers of this site.

If you are a teacher, keep an eye on this website: PDF versions of all the articles will soon be available, along with an e-book of the first round of articles for use in the classroom.

 

Young minds

 

Sean

5 years old

USA

I love books and articles with wry humor, and think my father is the funniest guy in the world. My other love is mechanisms, and I am frustrated that I have not yet learned all the math needed to build a spaceship. But I am working on it, meanwhile honing my logical skills by reviewing.

 

C.J.

13 years old

Canada

I'm a Canadian girl who just began grade 8. I like reading, dancing, acting, swimming and multiple other activities. My favorite colours are green, blue, purple and black. When I grow up I want to be a teacher, geologist, palaeontologist or another kind of science researcher. My favourite subjects in school are French, music, geography, English and science

 

Henry

12 years old

California, USA

I am in 7th grade, and my parents are neuroscientists. I like to play sports, especially basketball. My favorite TV show is the Simpsons. When I grow up, I want to be an engineer and invent cool and important things.

 

 

Marin

8 years old

Cambridge, MA, USA

3rd grader who plays the piano and loves to sing and dance. She participates in Science Club for Girls and she and her Mom will be performing in their second opera this year.

 

 

Scientists

  • Our authors and team of associate editors are contributing to the transmission of scientific culture to a new generation.

Ray Dolan

Wellcome Trust Centre
for Neuroimaging

University College London

London, United Kingdom

I study how emotion influences decision making. I use a technology called fMRI which enables me to measure brain activity while people perform mental tasks. Outside of work I listen to jazz, rhythm and blues, and opera. I am an avid hiker, reader of literature and enjoy fly fishing.

 

Dar Meshi

Freie Universität Berlin

Berlin, Germany

Doing neuroscience research is fun! I conduct experiments to understand how we make decisions when we interact with other people. I want to understand how we value other people's opinions and how their opinions can motivate our behavior. When I'm not doing science, I like to draw odd geometrical shapes, and I love watching movies as well.

Shelly
Levy-Tzedek

Medical Neurobiology Department

The Hebrew University

Jerusalem, Israel

Studies how we use our different senses (e.g., vision and audition), to understand our surroundings (e.g., that there is a yellow car approaching the crosswalk fast, and we should wait before crossing). We see the car, we hear its engine, and we plan our actions accordingly.

Jose M Carmena

Dept. of Electrical Engineering
and Computer Sciences

University of California

Berkeley, USA

Associate Professor of Electrical Engineering and Neuroscience at the University of California, Berkeley, and Co-Director of the Center for Neural Engineering and Prostheses at UC Berkeley and UC San Francisco. He is interested in how the brain controls movement, and in the design of neuroprosthetic systems for people suffering with paralysis and other neurological conditions.

Susan Riviera

Developmental Neuroscientist

University of California

Davis, USA

I study how thinking develops, particularly thinking about number, space, time and emotions or feelings. To do this, I study both typically developing people and people who have developmental disorders like autism and fragile X syndrome.

Robert Stickgold

Beth Israel Deaconess
Medical Center

Harvard Medical School

Boston, USA

He studies how sleep and dreaming make our memories stronger and last longer, while also trying to figure out what they really mean, and whether they are even worth keeping. His work suggests that sleeping is a big part of learning, and sometimes as important as studying!

José del R Millán

Center for Neuroprosthetics

EPFL

Lausanne, Switzerland

Professor at the Center for Neuroprosthetics of the École Polytechnique Fédérale de Lausanne (EPFL). He received a PhD in computer science from the Technical University of Catalonia, Barcelona (Spain) and has worked in Italy, US and Switzerland. He has received several awards for his work on brain-machine interfaces and brain-controlled robots.

 

Stephanie
Cacioppo

HPEN Laboratory

The University of Chicago

Chicago, USA

Director of the High Performance Electrical Neuroimaging (HPEN) Laboratory, Stephanie studies how one's social relationships modify one's brain, and vice versa. She has received several awards for her work on the science of social connection and pair bond.

Read more

call for papers

International Journal on Bioinformatics & Biosciences (IJBB)

Call For Papers

Bioinformatics is the application of information science and technology to the field of biology to increase the understanding of all biological process. The aim of this journal is to publish all the latest and outstanding research articles in all areas of bioinformatics and Biometrics. Researchers and scientists from the fields of biology, computer science, mathematics, statistics, and physics are invited to share their developments and new techniques in the fields of Biometrics and Bioinformatics. Topics of interest include, but are not limited to the following:

  • Biomedical modeling and computer simulation
  • Bioinformatics databases
  • Bio-grid
  • Biomedical image processing (segmentation, registration, fusion)
  • Bio-ontology and data mining
  • Parallel algorithms for biological analysis
  • Parallel architectures for biological applications
  • Phylogeny reconstruction algorithms
  • Protein structure prediction
  • Sequence assembly
  • Sequence search and alignment
  • Signaling and computation biomedical data engineering
  • Simulated annealing
  • Statistical analysis
  • Stochastic grammars
  • Support vector machines
  • System biology
  • DNA assembly, clustering, and mapping
  • Telemedicine
  • Computational genomics, Intelligence, proteomics, structural biology
  • E-health
  • Genetic algorithms
  • Hidden Markov models
  • Fuzzy logic
  • Molecular evolution and phylogeny
  • Molecular modeling and simulation
  • Molecular sequence analysis
  • High performance computing
  • Neural networks
  • Machine learning
  • Data visualization

Important Dates

Submission Deadline

  • 29 November, 2013

Notification

  • 28 December, 2013

Final Manuscript Due

  • 30 December, 2013

Publication Date

  • Determined by tde Editor-in-Chief

Contact

Read more

Your Life is an Algorithm

Humans, octopi and pine trees alike are all made up of cells, tiny but sophisticated systems that keep life going. Cells are almost like tiny factories run by robots, with the nucleus, DNA, proteins, lipids, and vitamins and minerals all playing critical roles. George Zaidan and Charles Morton lay out the blueprint of a cell and explain how biochemistry binds all life together.

1

About Author:

Dyani Lewis

  • I am a freelance science writer, broadcaster and podcaster based in Melbourne, Australia. My writing has been published in Cosmos online, The Conversation, Voice and Science Alert. I am the science producer for Up Close, the University of Melbourne’s podcast, and I am a regular co-host on Triple R’s Einstein-a-Go-Go. I’ve also written and recorded for ABC Radio National’s Ockham’s Razor. I occasionally tweet: @dyanilewis Read more about her

E_coli_metabolic_network

Metabolic networks are disected in systems biology (Photo credit: Wikipedia)

Science is very often about chipping away at a problem one component at a time. By piecing together fragments of knowledge on how each component of a system operates in isolation, an understanding of how the entire system works can emerge.

  • But systems biology — an emerging field of research in the life sciences — takes a different approach. It draws together and integrates large amounts of disparate data to take an encompassing approach to the study of life and its myriad processes.
  • Instead of looking at one protein, or unpicking a single biochemical pathway, systems biology embraces the complexity of an entire system to find patterns and networks in the data collected.  And from these patterns seeks to explain biological behaviour and function.
  • In the latest episode of Up Close I spoke to systems biologist  Dr Michael Inouye to talk about his field and how he goes about researching complex biological processes, such as disease.

Mike is a Senior Research Fellow and head of the Medical Systems Biology Lab with the Department of Pathology and Microbiology & Immunology, at the University of Melbourne. He is also an Honorary Senior Research Fellow at the Institute of Molecular Medicine Finland, at the University of Helsinki.

About Author:

Dyani Lewis

  • I am a freelance science writer, broadcaster and podcaster based in Melbourne, Australia. My writing has been published in Cosmos online, The Conversation, Voice and Science Alert. I am the science producer for Up Close, the University of Melbourne’s podcast, and I am a regular co-host on Triple R’s Einstein-a-Go-Go. I’ve also written and recorded for ABC Radio National’s Ockham’s Razor. I occasionally tweet: @dyanilewis Read more about her

Scionline

Open Registration is now full, use the lottery registration link to put your name in for a chance to register (to a lottery for 75 additional spots at the conference (registration fee still applies). Only one entry per person.

Dates for ScienceOnline Together 2014: Thursday, Feb 27 – Saturday, Mar 1, 2014

  • Total Registration is limited. Register early to guarantee your spot!

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The registration fee is due at the time of registration.

  • ScienceOnline Together 2014 Regular Registration Fee: $350
  • ScienceOnline Together 2014 Student Registration Fee: $300
  • (for high school through Graduate School students)
  • NOTE: It costs over $560 for each person attending ScienceOnline Together 2014. We are dependent on the generosity of our sponsors to cover the difference.
  • Historically, we’ve tried to make the conferences as affordable as possible. But we’ve had to reevaluate the actual cost of attending. We’ve also had to reevaluate the complimentary registrations that were given away for moderators. This fiscal review was necessary to ensure the ongoing sustainability of the conference.
  • Beginning with ScienceOnline Climate and ScienceOnline Oceans, we moved to a registration process that gives invited session facilitators a guaranteed spot at the conference in exchange for pitching in and helping with one session, but they pay their own way. We also are implementing a policy limiting an individual to moderating/facilitating only one session. This opens opportunities for more people to have a chance to help out with facilitating the conversations.

The ScienceOnline Together 2014 regular registration rate is $350 and the student rate is $300. We hope to attract some funding for scholarships for students and other community members in need. As we mentioned above, the actual cost for each attendee is over $560. We are still dependent on the generosity of sponsors who believe in our mission to make the conference possible.

For ScienceOnline Together 2014 the registration includes:

  • rock-solid wifi (which costs us about $35 per person!)
  • transportation from the hotel to the conference venue (The McKimmon Center, NCSU campus) for Thur, Fri, and Saturday in the morning and after sessions end each day
  • breakfast and lunch and snacks on Thursday, Friday, and Saturday (ask people who have attended—we try to have delicious food for a variety of diets)
  • Coffee, tea, and beverages non-stop throughout the day
  • Powerstrips in the session rooms!
  • Thursday night evening meal & activity ( still working on these !)

 

Registration Process

  • Registration will be first-come, first-served for the first 250 places.
  • Once those spots are filled, we will ask you to add your name to a lottery list (a form will be available at that time). There will be at least 75 lottery spaces. Lottery registration will remain open until November 22, 2013, Midnight EDT. At that time, we will have a random selection of the names submitted and notify everyone who is chosen. Lottery winners will have 73 hours to claim their spot. After that time, the registration spot will be offered to another on the list.
  • After the lottery, we will still accept names for the Waitlist (which automatically includes everyone in the lottery who did not get a space). If spaces become available (e.g., cancellations), we will invite people off the waitlist.
  • That doesn’t add up to 450 people! What about all the other spaces?
  • We have reserved spaces for moderators (1 moderator per session, and they can only moderate 1 session).

Cancellation Policy:

  • If you cancel your registration in writing by January 15, 2014, you will receive a full refund less a 15% processing fee. Email your request for cancellation to [email protected] (Twitter messages and FB messages will NOT be sufficient means for cancellation request). Registrations are not transferable.
  • Cancellation refund requests after Jan 15, 2014 will be considered if we are able to fill your spot from our Waitlist. A refund check for the amount of your registration (minus the 15% cancellation fee) will be issued after the conference. Nonattendance is not considered cancellation.
  • Please be sure to notify us if you cannot attend! There are others waiting to take your spot! We also need to coordinate last-minute cancellations of housing reservations, so that we can still retain the space in our block even if it is after the block deadline.

Sponsors

  • Many thanks to the sponsors for ScienceOnline Together 2014!
  • We’ll be adding sponsors on this page as they partner with us to make the conference the best it can be! If you are interested in sponsoring, please contact Karyn for more information.

Conference Host:


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For Registration/Read more click here

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