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Showing posts with label Education. Show all posts
Showing posts with label Education. Show all posts









This video belongs to Proteomics which is the study of proteins expressed by a genome. Bioinformatics is the analysis of biological information using computational and various statistical techniques. The journal provides an Open Access platform by OMICS Publishing Group to publish latest advancements in the field of proteomics and bioinformatics.In Proteomics & Bioinformatics, expert researchers explore this ever-changing field, providing the reader with a mix of review and methodology chapters which address the fundamentals of analysis methods, algorithms, data standards and databases. This supports the journals which publishes original research articles in all areas of experiment and applied proteomics & bioinformatics. In past years Journal of Proteomics & Bioinformatics has been showing tremendous citations and articles focusing the most advanced research trends. 


To access more information about Journal of Proteomics & Bioinformatics please follow OMICS Publishing Group's official page


















About Us
In a nutshell... This is the place to find out about, take part in, and contribute to science through recreational activities and research projects. Learn more about citizen science.

If you're a scientist or a representative of a citizen science organization or community group: This is the place to tell eager people about your work and get them interested in helping out.

Our Mission
SciStarter will bring together the millions of citizen scientists in the world; the thousands of potential projects offered by researchers, organizations, and companies; and the resources, products, and services that enable citizens to pursue and enjoy these activities. 

We aim to:
Enable and encourage people to learn about, participate in, and contribute to science through both informal recreational activities and formal research efforts.
Inspire greater appreciation and promote a better understanding of science and technology among the general public.
Create a shared space where scientists can talk with citizens interested in working on or learning about their research projects.
Satisfy the popular urge to tinker, build, and explore by making it simple and fun for people—singles, parents, grandparents, kids—to jump in and get their hands dirty with science.

Our Team



Darlene Cavalier
Founder

Darlene is also the founder of Science Cheerleader  a popular website and organization that works with 250 current and former NFL and NBA cheerleaders pursuing science and technology careers to promote science and the involvement of citizens in science and science-related policy. She has held executive positions at Walt Disney Publishing and has worked at Discover magazine for 15 years, where she now is a senior adviser and writer. She has created national science awards programs, science education initiatives, and a series of science-themed roundtable discussions for, among others, the Disney Institute, Space.com, Sally Ride's Imaginary Lines, and the Franklin Institute. She also serves on the Steering Committee for Science Debate and is a founding partner of Expert and Citizen Assessment of Science and Technology, which engages experts, stakeholders, and everyday citizens in assessing the implications of emerging developments in science and technology. She originated and managed the Emmy award-winning Science of NFL Football series produced by the NFL, NBC Sports, NBC Learn, the National Science Foundation and Science Cheerleader.
A former Philadelphia 76ers cheerleader, Darlene does not regret the years she gabbed through high school science classes. She earned a Master's degree at the University of Pennsylvania, studying science history, sociology, and science policy to learn more about people like herself: "hybrid actors," citizens interested in but not formally trained in the sciences. Discovering it was remarkably difficult to find opportunities to participate in science in any meaningful way, she launched SciStarter. Darlene lives in Philadelphia with her husband and four children, who have made it a hobby to explore the rainforests of Costa Rica. She's also a faculty associate at Arizona State University where she teaches a graduate course, aptly titled, Citizen Science.


Lily Bui 

Executive Editor

Lily Bui holds dual degrees in International Studies and Spanish from the University of California Irvine. She has worked on Capitol Hill in Washington, D.C.; served in AmeriCorps in Montgomery County, Maryland; worked for a New York Times bestselling ghostwriter; and performed across the U.S. as a touring musician. She currently works in public media at WGBH-TV and the Public Radio Exchange (PRX) in Boston, MA. In her spare time, she thinks of cheesy science puns. Follow @dangerbui. 



Jenna Morgan Lang

Editor, Featured Projects and Newsletter

Dr. Jenna Lang spends her days exploring the various means by which microbes rule the world. She has worked with Jonathan Eisen since 2006, first as an employee of the DOE Joint Genome Institute, then as a Microbiology PhD student, and now as a permanent fixture in his lab at UC Davis. Jenna became hooked on Citizen Science while working with Darlene on Project MERCCURI, and now aims to include a citizen science component in all future research projects. For fun, she likes to play poker, at the Bellagio, in her wedding dress.



John Ohab

Contributor

Dr. John Ohab is a digital strategist at the U.S. Naval Research Laboratory. John was previously a new technology analyst at the Department of Defense  Public Web Program, providing research and evaluation of web technology initiatives. He also led Defense Department's award-winning outreach project, “Armed with Science,” a cross-agency effort to connect military scientists and engineers with the public through social media. John joined the government through consecutive American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellowships at the Department of Defense (2008) and the National Institute of Mental Health (2007). John received his B.S. in biopsychology from UC Santa Barbara in 2002 and his Ph.D. in neuroscience from UCLA in 2007. John was born and raised in Tempe, Arizona, experienced a moderately successful run in high school varsity tennis, and is waiting patiently for that elusive Arizona Cardinals Super Bowl victory.


Mark Severance

Director of Space-based citizen science projects

Mark Severance is SciStarter’s Space Guy and he has been a Space Guy all of his life. A NASA engineer at the Johnson Space Center in Houston, Mark has spent most of his career in Mission Control Center-Houston as a Flight Controller for the Space Shuttle and International Space Station. He also spent time in Mission Control Center-Moscow as a NASA Operations Lead early in the ISS program and when NASA had Astronauts working onboard the Mir space station. He has had a life-long interest in spaceflight and views the space program as a catalyst for engaging minds of all ages in a deeper understanding of science, engineering, technology and mathematics. Mark holds BS degrees in Physics and Electrical Engineering from SMU and MS in Physical Science, with a concentration in Orbital Mechanics, from the University of Houston. He began his hands on interest in space as teenager through his radio tracking of Soviet and Chinese human and robotic spacecraft in conjunction with the Kettering Group. He credits his satellite tracking as the most directive force in his educational and professional careers. Mark is currently a NASA engineer and manger for a space communications lab at the Johnson Space Center. Previous to this assignment, he worked in NASA’s Office of Education to start a program of educational activities and experiments onboard the ISS. He is heading up SciStarter’s in-development suite of space-related, citizen science projects.


Jonathan Brier

Strategic Advisor

Jonathan Brier is citizen science enthusiast from Michigan who enjoys working with Internet connected technologies a little too much. He holds a M.S. in Information and specialized in social computing from the University of Michigan School of Information and a B.S. in Media and Communication technologies from Michigan State University. His interest for science began with his continued use of the word “why” for which his father an engineer and mother a teacher took the time to give an explanation that would make any scientist proud. Jon’s citizen science passion began with his discovery of the SETI@home distributed computing project after watching the movie Contact. This branched to all things citizen science as he learned of more ways science research could harness public participation. Outside his day job as a User Experience Researcher at the University of Michigan, he works with GridRepublic on BOINC powered distributed computing projects and scours the Internet for anything and everything related to citizen science. He hopes to bring added enthusiasm and expertise to SciStarter.


Caren Cooper

Contributor

Dr. Caren Cooper is also a blogger for Scientific American and the Public Library of Science. She is a research associate at the Cornell Laboratory of Ornithology and Senior Fellow in the Environmental Leadership Program. She is co-chair of the publications committee of the newly forming Association for Citizen Science and co-editor of an upcoming special feature on citizen science in the open-access journal Ecology & Society. She has authored over 35 scientific papers, co-developed software to automate metrics of incubation rhythms, and is co-creator of NestWatch, CamClickr, Celebrate Urban Birds, YardMap, and the House Sparrow Project. Follow her @CoopSciScoop. She likes to propel herself on one wheel, two wheel, and eight wheel devices.



Nick Fordes

Contributor

Nick Fordes is a science enthusiast who enjoys doing, teaching, and communicating science.  Nick recently graduated from the University of Idaho with an M.S. in Water Resources.  His research involved creating a web-based participatory GIS application for use in watershed management. He has a true love for technology and appreciation for what the web-based communications can do for promoting science and increasing science literacy.   Nick most recently worked with the Council for Environmental Education, developing K-12 environmental science based curriculum.  In his spare time, Nick enjoys biking the bayous in Houston and fishing as often as he can.  He has been known to use his scientific knowledge to make a pretty mean brisket.



Lisa Gardiner

Contributor

Dr. Lisa Gardiner enjoys exploring the Earth from the tops of Colorado’s mountains to the bottom of tropical seas. She has a background in earth science, climate science, ecology, and paleontology - receiving her B.A. from Smith College in Geology and Marine Science and her Ph.D. from University of Georgia in Geology. She is currently honing her skills writing about science in the M.F.A. program at Goucher College. Lisa started Citizen Science Buzz, a blog on Talking Science to share exciting stories about how the public is getting involved with science. Lisa also develops resources for the public, students, and teachers to learn about the earth at Spark, UCAR Science Education. She has written for educational websites, led workshops for teachers, taught environmental education, and occasionally helped develop museum exhibits. She is the author and illustrator of several books and articles about science for children. For several years, Lisa’s eyes were glued to fossil coral reefs in the Bahamas as she searched for tiny clams and snails to study for her dissertation. Now she lives a mile above the ocean in Colorado and is a fan on hiking in summer, whether through mountain tundra or through city blocks, and skiing and snowshoeing in winter. When wearing her artist hat, Lisa creates painting of trees (or forests, depending on your perspective).


Pete Madden

Contributor


Pete Madden is a freelance journalist based in Los Angeles, California. He holds an M.S. in Digital Media from the Columbia Journalism School and a B.A. in Communication Studies and English from Vanderbilt University. He is currently Content Coordinator at Escape Apps, a tech startup that creates travel and local discovery smartphone apps, and he has worked for the Los Angeles Times, ABC World News with Diane Sawyer, and Regis High School, a tuition-free prep school in New York City. An avid swimmer and diver, Pete has been lucky enough to explore the reefs in Australia, Belize, and the Galapagos, and when he's not writing about citizen science, you can find him planning his next underwater adventure.














Welcome to ß-Lactamase
Beta-lactamases are enzymes  produced by some bacteria and are responsible for their resistance to beta-lactam antibiotics like penicillins, cephamycins, and carbapenems (ertapenem) (Cephalosporins are relatively resistant to beta-lactamase). These antibiotics have a common element in their molecular structure: a four-atom ring known as a beta-lactam.









In the last ten years, the open source R statistics language has exploded in popularity and functionality, emerging as the data scientist's tool of choice. Today, R is used by over 2 million analysts worldwide, many having been introduced to its elegance and power in academia. Users around the world have embraced R to solve their most challenging problems in fields ranging from computational biology to quantitative finance, and to train their students in these same fields. The result has been an explosion of R analysts and applications, leading to enthusiastic adoption by premier analytics-driven companies like Google, Facebook, and and the New York Times.











Interview Dates28-29 August 2013, EMBL Grenoble
28-30 August 2013, EMBL-EBI Hinxton
28-30 August 2013, EMBL Hamburg
29-30 August 2013, EMBL Monterotondo
02-04 September 2013, EMBL Heidelberg

Spring Recruitment 2014

Call for applications for the Spring Recruitment 2014 is now open. Please apply here.
Information to applicants: The EMBL does not charge a fee at any stage of the recruitment process (application, interview meeting, processing, training or any other fees). The EMBL does not concern itself with information on bank accounts.
Application opens12 August 2013 CET (GMT +1)
Registration Deadline11 November 2013, 23:59 CET (GMT +1) 
via the Online Application Form.
Submission Deadline18 November 2013, 23:59 CET (GMT +1)
Reference Deadline20 November 2013, 23:59 CET (GMT +1)
Interview DatesWill be published closer to the time.
Full details about the interview procedure will be sent only to invited candidates.

Reference Requirements

You can submit your application irrespective of the fact if your referees have completed the online reference form or not, as the submission does not impede referees access to the application.
Referees must submit their online references by latest 20 November 2013, 23:59 CET (GMT +1). We strongly suggest that you complete the 'general info' and 'references' part of the online application first in order to give your referees enough time to complete the reference online. Furthermore please make sure to contact your referees before completing this part in order to find out if they are available and willing to provide a reference. It is applicant's responsibility to ensure that references reach us on time.
As stated within the online application form we only accept references provided through institutional email accounts.
Only in cases where the referee does not have one, i.e. only holds a 'hotmail', 'gmail' etc. account, we ask you to:
  1. Complete the form with the available email address.
  2. Inform your referee NOT to complete the online form.
  3. Ask your referee to send a reference letter on institutional headed paper as a PDF document topredocs@embl.de
  4. Ask your referee to include your application ID number (5 digits) in the reference letter.
Read more @ EMBL








A new computational method for working out in advance whether a chemical will be toxic will be reporting in a forthcoming issue of the International Journal of Data Mining and Bioinformatics.
There is increasing pressure on the chemical and related industries to ensure that their products comply with increasing numbers of safety regulations. Providing regulators, intermediary users and consumers with all the necessary information to allow them to make informed choices with respect to use, disposal, recycling, environmental issues and human health issues is critical. Now, Meenakshi Mishra, Hongliang Fei and Jun Huan of the University of Kansas, in Lawrence, have developed a computational technique that could allow the industry to predict whether a given compound will be toxic even at a low dose and thus allow alternatives to be found when necessary.
Toxicity is almost always an issue of availability and dosage. Whether or not a compound is natural or synthetic it can be toxic from snake venom and jellyfish stings to petrochemicals and pesticides. However, some chemicals are more toxic than others, exposure to a lower dose will cause health problems or potentially be lethal. It is very important to find a way to determine whether a newly discovered synthetic or natural chemical might cause toxicity problems.
The team also points out that the US Environmental Protection Agency (EPA) and the Office of Toxic Substances (OTS) in the USA had listed 70,000 industrial chemicals in the 1990s, with 1000 chemicals added each year for which even simple toxicological experiments had not been carried out. This is largely a problem of logistics and costs as well as the ethical question of whether so many tests, which would have to be carried out on laboratoryanimals, should be done at all.
Now, Huan and colleagues in the Department of Electrical Engineering and Computer Science at Kansas, have successfully tested a statistical algorithm against more than 300 chemicals for which the toxicity profile is already known. Their technique offers a computational method of screening a large number of compounds for obvious toxicity very quickly and might preclude the need for animal testing of the compounds, provided regulators don’t insist on such “in vivo” data from the latter.
The research builds on well-established principles from the pharmaceutical industry known as Quantitative structure-activity relationships (QSARs) in which the type of atoms and how they are connected together can be correlated with the activity of a drug molecule. Certain molecular shapes and types are soluble in water, for instance, or interact in a certain way with different enzymes and other proteins in the body, leading to their overall activity. Different molecular features will make a similar molecule behave in a different way – more or less soluble, stronger or weaker acting. The team has now turned the QSAR around so that instead of searching for the features in a molecule that make it of benefit in medicine they look for the atomic groups and the type of bonds that hold them together to find associations with toxicity.
The team points out that few earlier attempts at predicting toxicity of chemicals have proved successful, most approaches are no better than random guessing. The team’s new statistical approach combines “Random Forest” selection with “Naïve Bayes” statistical analysis to boost the predictions well beyond random. They team saw prediction accuracy in 2 out of 3 chemicals tested. Given that there are around 100,000 industrial chemicals that need toxicity profiling, this result should allow the industry and regulators to focus on a large number of the most pressing of those, the ones predicted to have greatest toxicity and leave the less likely until additional resources are available.
The researchers are now tuning the algorithm to work faster and with greater precision so that it ignores common molecular features now known not to contribute to toxicity characteristics in the chemicals they have studied so far.
As Britney Spears asked in her song: “Don’t you know that you’re toxic?” Well, we do now.
“Computational prediction of toxicity” in Int. J. Data Mining and Bioinformatics, 2013, 8, 338-348
Source of the article 


ISCB Community News
F1000Research is an online life science journal, which enables articles to be updated post-publication, through the use of versioned papers. The journal is waiving all charges for bioinformatics software papers submitted before 31st December 2013. This is great news for both developers and users of bioinformatics tools; as incremental improvements and updates to software are released, these can be documented through a set of F1000Research-threaded papers.

F1000Research is novel in many of its approaches to science publishing. Once an article has passed editorial checks, publication is very fast, typically under 7 days following final submission. Articles undergo formal transparent peer-review, post-publication, with all reviews and any resultant discussion being documented as part of the article. The journal also requires all papers to include the underlying data, and all good science is accepted, regardless of perceived impact at time of publication.


The threaded papers approach enables developers to minimize the time spent on the important (but time consuming) job of disseminating documentation, whilst also demonstrating to funding bodies a commitment to ongoing engagement with users. Furthermore, it shows users that a tool is being actively maintained and improved.


To encourage bioinformatics tool developers to try this new way of publishing, F1000Research are waiving all article processing charges for such life science software papers submitted before the end of 2013. The fee waiver includes subsequent updates; just put the code SOFT13 in Section 6 of the simple one-page submission form. If you are using LaTeX to write papers, there is also a one-click submission option from the F1000Research LaTeX template, hosted by the online collaborative LaTeX editor writeLaTeX.


So how about providing an F1000Research threaded publication for your bioinformatics tool, allowing you to update the paper as you improve your software?


More information about F1000Research can be found at http://f1000research.com/

More information about threaded software papers can be found at http://blog.f1000research.com/2013/07/22/document-your-software-updates-with-f1000research/
The writeLaTeX F1000Research template can be found at https://www.writelatex.com/templates/41-f1000research-journal-article-template

URL:
http://f1000research.com/

Contact Person: Michael Markie (
michael.markie@f1000.com)





Overview

This course will provide an overview of key issues that affect metabolomics studies,bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.

Audience

This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

Syllabus, Tools and Resources

During this course you will learn about…
  • Metabolomics study design, workflow and sources of experimental error
  • Metabolomics data processing: R, XCMS, MetFrag, NMR tools, …
  • Metabolomics data analysis: R, Bioconductor, data fusion, univariate and multivariate data analysis, data clustering and correlation methods…
  • Metabolomics downstream analyses: MetExplore, Cytoscape plugin, metabolic pathway analysis, visualisation, differential expression, metabolomics flux.
  • Metabolomics standards and databases: data dissemination and deposition in EBI-MetaboLights, ISATools and COSMOS

Learning Objectives

After this course you should be able to…
  • Discuss major principles of metabolomics experimental design and factors that impact upon subsequent analysis
  • Identify strengths and weaknesses in a variety of metabolomics analytical approaches
  • Use a range of Bioinformatics software to pre-process, process and analyse metabolomics data
  • Discuss current trends and challenges in metabolomics
Application registration closes 17 January 2014 (12:00 midday GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 31 January 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.

Contact: 
Reza Salek EMBL-EBI & Cambridge University, UK













The Search for America's Next Top Young Scientist 

The 2013 Discovery Education 3M Young Scientist Challenge asked students to create a 1-2 minute video describing a new innovation or solution that could solve or impact an everyday problem related to how we live, how we work or how we play. Ten finalists were chosen for their passion for science, spirit of innovation and communication skills. Here, you can meet the finalists and follow their summer adventures by reading their blog entries!
 
 
Read more














Infographics animated video simplifying the role of Systems Bilogy in biological research. produced for the Weizmann Institute of Science.












Open Source or Free Bioinformatics Tools
  1. HD-CNV (Hotspot Detector for Copy Number Variants)  source
  2. bedTools – source
  3. PennCNV – source
  4. Circos – source
  5. FigTree – source

R and R packages
Basic statistics in R
  1. ape – source

Other Nifty Free Downloadable Software
  1. Notepad ++ - source
  2. Mendeley – source
  3. JabRef – source

Perl-based tools
  1. pedigree-perl (prepares a TeX file) – source

Typesetting, Formatting, Graphing, Images
  1. TeXStudio – source
  2. Venn Diagram Plotter – source

Databases and Browsers
  1. NCBI (general) – source
  2. dbVar – source
  3. Centre for Genome Dynamics (The Jackson Laboratory) – source
  4. UCSC Genome Browser – source

Proprietary Licensed Software
  1. Partek Genomics Suite – source