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Posts from the ‘10 tips’ Category

Youtube: Top 10 Videos About Genetic Conditions

We all know how important it is to inform people about genetic conditions. I’ve created several articles and tried to list several sites and resources that could be useful for people with genetic conditions and for their relatives (see below). One of these resources is Youtube where I found some interesting videos focusing on the genetics of medical conditions. Please let me know if you happen to know more.

Further reading:

New Tips: How to search for genetic conditions

Last year, I came up with a list containg 10 tips on how to search for genetic conditions. Now, after weeks of tagging and browsing, I’d like to improve that list with some new tips. But this time, I’d like to show you databases dedicated not only to genetic conditions, but gene-disease associations and human genome epidemiology as well.

A global collaboration of individuals & organizations committed to the assessment of the impact of human genome variation on population health & how genetic information can be used to improve health & prevent disease.

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It provides access to a continuously updated knowledge base in human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests.

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GAIN is taking the next step in the search to understand the genetic factors influencing risk for complex diseases. Through a series of whole genome association studies, using samples from existing case-control studies of patients with common diseases, GAIN will contribute to the identification of genetic pathways that make us more susceptible to these diseases and thus facilitate discovery of new molecular targets for prevention, diagnosis, and treatment.

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It archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.

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A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. You should also check out the Disease-Gene mapping tool.

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It will conduct genome wide association studies and analyses in several large NHLBI Cohort studies to identify genes underlying cardiovascular and lung disease and other disorders like osteoporosis and diabetes.

Let’s finish with a great idea, the human disease network published at PNAS.

A network of disorders and disease genes linked by known disorder–gene associations offers a platform to explore in a single graph-theoretic framework all known phenotype and disease gene associations, indicating the common genetic origin of many diseases. Genes associated with similar disorders show both higher likelihood of physical interactions between their products and higher expression profiling similarity for their transcripts, supporting the existence of distinct disease-specific functional modules.

Let me know please if you happen to know more useful databases and tools.

Further reading:

10 Tips: Christmas Gifts for Science Geeks!

Just 2 days to go before Christmas, so here is a list of possible ideas and gifts that a real science geek should buy or should get…

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What are your tips?

A couple of more ideas:

Top 20 Facebook Applications in Science and Medicine

logo_facebook.jpgFacebook is a social networking site with several thousands of applications that you can add to your profile. While some of the biggest stories in the news are about the future of this community site, I thought I should create a collection of useful applications from the field of medicine, science and web 2.0. Enjoy!

Health and Medicine:

  • Medline Publications: List your Medline-listed academic publications on your Facebook profile, and view your friends’ publications as well!

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  • Med Tracker: Use Med Tracker to share your ratings of prescription and over the counter drugs.

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  • Healia Health Challenge Quiz Game: You can test your health knowledge with this interactive health quiz game. Challenge your friends to see who knows more about health and medicine. You start with being Pre-Med, then you can become Medical Student and maybe, the “Chief of Medicine.”

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  • Support the Red Cross: Every day that you click on the Donate button on the Red Cross toolbar, will donate money to the Red Cross. They’ll donate 1$ for every 200 points people submit each day.

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  • Mobile Health Coach: It’s a health coach that gives you tips throughout the day on how to live a fuller, happier life.

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  • Awareness Ribbons: Now you can wear your ribbons on your Facebook profile! You can choose from 300+ causes and concerns. Ribbons automatically link to Wikipedia so people can learn more about your causes.

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  • Quit Smoking: This application helps you give up cigarettes and stop smoking. Set up your own quit smoking program in minutes, give yourself a reward target to spend the money that you’ve saved on and record your daily progress. If you follow the plan provided, you’ll be able to buy yourself that reward on the date indicated.

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  • PersonalDNA: A personality test that combines thorough scientific analysis with novel questions and response techniques. Find out which one of the 256 personality types matches you, and get details that go beyond those categories, plus suggestions on how to be different.

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  • Be an organ donor: There is always a desperate need for more organ donors. The success of transplants depends on the generosity of donors and their families. Residents of the UK and USA can become donors by filling out a form online.

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Science:

  • Science Videos: A unique video search engine for science videos where every video is screened and approved based on accuracy and quality by scientists.

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  • Family Tree: Build your Family Tree including your relatives both on and off Facebook. Add unlimited generations of all possible ancestors. Upload a photo for each relative or simply use their Facebook profile photo. Display your tree and feature your family and heritage directly on your profile page.

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  • OneFamilyTree: Build your family tree online and share it among your friends and relatives. You can upload GEDCOM files, customize the family tree or search for your ancestors.

  • NASA Astro Photo of the Day: Displays the NASA Astro Photo of the Day. A daily display of fantastic astronomical images chosen by the NASA.

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  • F@H Protein Researcher: Folding@Home is a computer program designed to aid scientists in medical research by distributing computationally-intensive tasks to home desktops all over the world. Specifically, the Stanford University developers’ goal is “to understand protein folding, misfolding, and related diseases,” and has made progress in understanding diseases such as cancer, Alzheimer’s disease, Huntington’s disease, and Parkinson’s disease.

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Web 2.0:

  • Blog RSS Feed Reader: It allows you to add a personal blog or corporate blog RSS Feed to your Facebook profile for your friends to read. It’s a great way to drive traffic to your blog. It works with popular blogging platforms such as Myspace, MSN Live Spaces, WordPress, Blogspot, Typepad, Movable Type, Textpattern and more.

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  • My Wikipedia: It allows you to display sections of Wikipedia on your profile page. By default, My Wikipedia displays the daily “Featured Article” from Wikipedia’s main page, but can be customized to display any article of your choosing.

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  • Second Life Link: This application integrates Facebook with the most popular Virtual World – Second Life™! You can show your Second Life Avatar to your friends, view online status of your Second Life friends or just share your virtual home and your favourite virtual places with them.

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  • StumbleUpon: StumbleUpon is the best tool to discover and share great websites. If you add StumbleUpon to your Facebook profile, you can share your favourite weblinks and you can also Stumble your friends’ Favourites by checking out your What’s New tab.

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I hope you enjoyed this selection and please let me know if you happen to know more Facebook applications in the field of medicine or science!

10 Reasons Why Nature is the Best in Science 2.0

In the era of web 2.0, we have plenty of opportunities of education and communication in either science or medicine. In this special field (often called science 2.0), Nature Publishing Group has become the leading force and I’ve got 10 reasons for that.

  • Scintilla: Scintilla collects data from hundreds of news outlets, scientific blogs, journals and databases and then makes it easy for you to organise, share and discover exactly the type of information that you’re interested in. You can rate items and recommend them to any colleagues who’ve also signed up to the site.

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  • Precedings: Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by professional curation team for relevance and quality, but are not subjected to peer review.

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  • Nature Network: Nature Network is the online meeting place for scientists to gather, talk and find out about the latest scientific news and events. Science is an international endeavor and deserves a global stage for discussion. Scientists can also benefit from interactions at the local level.

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  • Connotea: Free online reference management for all researchers, clinicians and scientists. Tags make the difference! Connotea can quickly save and organize links to your references, moreover you can follow the new additions to a tag by RSS.
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  • Nature 2.0: Joanna Scott does a perfect job on Second Nature, the island of Nature Publishing Group in Second Life. Unique speakers, sessions, conferences. We hold our SciFoo lives on sessions on the Second Nature island as well.

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  • Web feeds: You can follow easily the research, reviews, clinical practice and other NPG journals.

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  • Podcasts: A podcast is an audio file with which it becomes even more easier to follow the content of a journal. Each week Nature publishes a free audio show in the field of genetics, physics, medicine and many more.. Every show features highlighted content from the week’s edition of Nature.

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  • Dissect Medicine: Dissect Medicine is a collaborative medical news website, which indexes and ranks international medical news. It spans general interest articles to basic research. Dissect Medicine users submit news items for review with tags and keywords. These are then ranked by the user group. This ensures that only the most relevant, and influential articles will make it as a current headline story.

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  • OTMI: It aims to enable scholarly publishers, among others, to disclose their full text for indexing and text-mining purposes but without giving it away in a form that is readily human-readable. It provides for a range of structured disclosure options, from word vectors (lists of word occurrences with frequency counts) and the presentation of text ‘snippets’ out of narrative order, to the presentation of full text in ‘raw’ or ‘reduced’ form.

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I’m proud to be a member of Nature Group in Second Life. I’m pretty sure Nature will rule the next few years in science 2.0. Maybe, they should make some more steps in order to become the leading force in medicine 2.0 as well, but that’s my problem. Last, but not least, take a look at these interesting posts:

Leave a comment if you don’t agree with me and would like to present an other platform of science 2.0.

Medicine in Wikipedia: Reliable Information?

I’ve already talked a lot about the medical articles of Wikipedia and Citizendium. As an administrator, I’d like to provide some useful tips for those who, as a layman or a medical professional, would like to be involved in improving the medical articles of Wikipedia. Second, I’d like to show you how Wikipedia is improving in the aspect of credibility.

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So, let’s see some tips on how you can join the medical editorial board in Wikipedia:

Why do I say bravely that Wikipedia is improving in the aspect of credibility and reliability? As I tried to be objective, I chose some of the first entries in the List of causes of death by rate article and determined the number of references and external links in each article now and a year ago. Here is the result:

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For me, it proves that Wikipedia is still improving regarding the number of references which is one of the most important aims nowadays in this huge community.

Citizendium, the online encyclopaedia that only selected editors, professionals can edit, is, obviously, more reliable than Wikipedia, but Wikipedia is far more comprehensive than Citizendum. So both should serve as an additional source of information, but never as your last source

Further reading:

Open Letter to the Physicians of the World

Dear Medical Professionals,

I’m writing to you to describe why to use web 2.0’s features in your practice.

I’m pretty sure web 2.0, the new generation of web services, will play an important role in the future of medicine. These web tools, expert-based community sites, medical blogs and wikis can ease the work of physicians, scientists, medical students or medical librarians. We, medical bloggers, believe the new generation of web services will change the way medicine is practiced and healthcare is delivered.

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In the field of medicine, the most important thing is to get the right information in time. With the tools, services and sites of web 2.0, it’s getting easier and even more comfortable. Those physicians, who want to be up-to-date in their fields, should be open to the improvements and new opportunities of the world wide web.

Let’s take a look at how you can use these tools in your own practice.

Most physicians and scientists I know, go back to PubMed from time to time and search for the old terms to see whether there are new additions to the database. If you use the Save Search function, you can get your PubMed updates via e-mail or RSS. You don’t have to search again and again, just sit back and wait for the next letter containing the newest articles in your field.

If you have to track more and more papers and online journals, then you should start using RSS. It’s the best and most comfortable way of getting the selected information automatically what means you can read the articles of medical journals in one place.

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Medical blogs (web log or internet diary) provide content and express opinion on healthcare that you can never find in a medical paper. As there are plenty of medical blogs out there, and you definitely don’t have enough time to run through all of these blogs and other sites, so blog carnivals are created for you! These carnivals collect the best posts on a subject from time to time.

Reading blogs is even easier and more comfortable with podcasts and videocasts. A podcast is a portable audio file (a videocast is a video file) that you can listen to while working, doing exercises or just sitting in a traffic jam. And these are just some examples of the features of web 2.0, or the so-called medicine 2.0.

You can also take part in constructing the future of medical education in Second Life, the virtual world. Train medical students and nurses in the virtual medical center.

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You can browse among the great medical wikis created and maintained by physicians from around the world (you may start with Ask Dr Wiki). These are databases specifically constructed for physicians who are not IT experts but would like to search easily for medical terms. Moreover, search engines (like Google, Yahoo) don’t select among sources, so many of the medical search results can’t be relevant. But medical search engines use peer-reviewed sources and sites selected by experts providing the most relevant and reliable medical information of the best quality.

Web 2.0 is based on communities and collaboration, that’s why you should join one of the best medical communities at Tiromed.com. Ask a mentor or become a mentor. Upload your CV and find collaborators from around the world, or find a job via this community.

I hope you’re going to be open to these opportunities and you’re going to understand why it’s so crucial to use these tools to keep yourself perfectly up-to-date in your field. Let me know please if you have any kind of questions or would like to know more about these tricks and methods. I’m looking forward to reading your answer.

Regards,

Bertalan Meskó
Medical Student
Medical and Health Science Centre
University of Debrecen

http://Scienceroll.com

How to create a blog carnival: Step by Step

I know well how hard it is to run through all of your favourite blogs every day if you have a lot in mind. That’s why bloggers create blog carnivals for your pleasure, dear reader! If you are a blogger and you plan to create a blog carnival dedicated to your field of interest, here is a HOWTO guide:

  • Find out a proper name: For example, our carnival of genes and gene-related diseases is called Gene Genie; the genetic carnival is Mendel’s Garden; our medical web geekery carnival’s name is Medicine 2.0 and the best medical carnival is Grand Rounds. It’s important to make it easier to find out the main goal of the carnival just by it’s name.
  • Register it at BlogCarnival.com: The best place for carnivals. You can easily organize your editions, set up new ones and get the submitted articles automatically. And they also feature carnivals on the main page.

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A screenshot from Medicine 2.0’s blogcarnival.com page

  • Create a blog for your carnival: It’s good to have an archive of your edition. I mean you shouldn’t post there the entire editions (due to search-engine optimization reasons), just short abstracts and links. It’s easy to follow the editions, to know who will host the next one and where we can submit our articles. Take a look at our Gene Genie archive!

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Our Gene Genie archive page

  • Write a mission statement and a guideline: It’s important to know who can host your editions, what kind of articles should be included and what the carnival’s main goal is. If you make it clear the first time, you won’t get submissions which have nothing to do with your field of interest. It’s also worth launching a carnival on an uncovered topic.
  • Create a logo: A logo can be crucial when you would like to indicate the field you’re writing about just by the name of the carnival or a logo. For example, we were lucky to have Ricardo Vidal at My Biotech Life who is a great logo-creator. And our Gene Genie logo tells you everything you have to know about our carnival.

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Many thanks to Ricardo Vidal for the logo!

  • Recruit: That’s not enough! You need bloggers, participants to host your editions , to submit their articles. When you launch a new blog carnival, you won’t get any submissions, so you’ll have to find a lot of interesting posts, articles and send it to your next host in time. It takes time and energy.
  • Be patient and work hard: It’s still not ready. A blog carnival is considered a reliable carnival after about 10 editions. So be patient, work hard each week to find enough submissions; help your hosts as much as you can to make sure they’ll enjoy hosting your carnival.

And you will be the founder of a useful, high-quality blog carnival which helps your readers to find the best articles on a specific subject; and helps your blogger fellows how to promote their own articles.

If you have any kind of question, drop me a line (berci.mesko [at] gmail.com)!

How and Why to use Second Life for Education?

Do you think Second Life, the virtual world is still about gambling and pornography? Forget it! While gambling is being forbidden in SL, education has it’s golden age. Let’s see why we should use Second Life for education:

  • Collaboration: You can contact people of the same field of interest from around the world.
  • Without boundaries: You can work with people without boundaries (neither technical or geographical).
  • Interactivity: It’s better than a videoconference because you can use videos, presentations, images and weblinks at the same time in one place. It means you can easily create links between in-world activity and real-world information resources.
  • Support: If you’re a patient, you can easily find people dealing with the same problems. You can meet them virtually, discuss your problems, listen to doctors attending in SL.
  • Learning: In some fields, there are just a few experts and it’s far not simple to find them in real. But in SL, it becomes possible by presentations and e-learning tools. You can also use tutorials.
  • Search: You can do PubMed searches or you can browse among the many books of the virtual libraries.
  • Exhibits: How could you create an exhibition in a videoconference or a website? Well, you could, but it’d be complicated while in SL, it works like that:

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And how can we use Second Life for education? Here are some examples:

  • Ann Myers Medical Center: a virtual medical training center where medical education gets a unique opportunity to find new ways in training medical students. During the first exercises, I could learn more about medical cases with images, videos, patient stories and weblinks. I’ve had a chance to discuss those cases with medical students and physicians from around the world. (Teleport!)

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  • SciFoo lives on session: This is the perfect example how to do something virtually when you have no chance to do it in reality. I couldn’t participate in such a great conference like SciFoo was, but now I’m the co-organizer of this virtual session with Jean-Claude Bradley. I’ve already presented my slideshow about web 2.0’s impact on medicine at several clinics and department at my university. Through SL, I could present it to people from Nature Precedings, Connotea, Biowizard.com, Tiromed.com and scientists, physicians from around the world. It was a unique experience for me.

  • Genomic Island: Max Chatnoir has been working hard to create such an interesting and useful island totally devoted to the education of genetics and genomics. Several floors with genetic quizes, images, virtual experiments, texts, videos and plenty of links to genetic resources. (Teleport)

  • Drexel University: Jean-Claude’s main project: “With the growing popularity of gaming, we anticipate that more students and faculty will use virtual platforms like ‘Second Life’ to extend the education experience. On this platform — where anything is possible — the Library gets to explore new ways of supporting academic programs, research and student learning, limited only by the scope of the imagination.” Anyway, Harvard, Stanford and MIT are among the universities using SL. This is the example of how to construct a real university’s virtual form.

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The blue obelisks are an interactive quiz

  • Learning languages: Plenty of tutorials, texts, links, online learning groups.

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  • Presenting slideshows: There are many rooms, sites and buildings created for conferences, meetings, etc.

meetingeducation.pngThere are so many other examples, I only wanted to persuade some educators and students to give it a try as Second Life is going to become one of the best tools for education.

Related posts:

7 Tips: How to track the information you need!

Recently, some of the researchers here in Debrecen have asked me how they could track the changes of their field of interest. Even in the field of medicine or science, it’s crucial to be up-to-date and to find methods/tools that can make your work easier and more comfortable. So here are some tips on how to track the information you need, how to be up-to-date in your field.

  • PubMed Save Search:

Most of the physicians and scientists I know, go back to PubMed time by time and search for the old terms to see whether there are new additions to the database. If you use the Save Search function, you can get your PubMed updates via e-mail or RSS. You don’t have to search again and again, just sit back and wait for the next letter containing the newest articles in your field. How? Create an NCBI account, make your regular search and click on the Save Search button:

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Then edit the preferences, that’s all:

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  • Third-Party PubMed tools:

I couldn’t come up with a better expression. These sites/tools are based on PubMed but try to open new ways in searching for different scientific/medical terms. For example, NextBio is a scientific data search engine with which you can use PubMed in a more dynamic way. The CureHunter provides interactive network graphs of related drugs, diseases and therapies. Or take a look at PubMed Reader, a free web-based research program for displaying PubMed / Medline search results on an individual basis. It means you can create your own up-to-date Medline and PubMed literature search.

David Rothman has a lot more!

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Screenshot of CureHunter

  • Use RSS or webfeed!

If you have to track more and more papers and online journals, then you should start to use RSS. It’s the best and most comfortable way of getting the selected information automatically what means you can read the articles in one place. If you don’t believe me, just take a look at some of my interviews with famous bloggers and see how many blogs/journals they follow every day. How? All you need is a feed reader program (like feedreader.com) or log in to your Bloglines, Google Reader or Netvibes account. Then open your favourite medical/scientific journal or blog and click on the feed icon:

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Insert that link into your program; browser or online tool and you made it. Let the information come to you!

  • Use an even better RSS!

Alan at Science of the Invisible pointed out the features of Aide RSS, a new service which is actually a web 3.0 application.

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The service filters the RSS noise by scoring each post by the number of comments it received, number of times it’s been tagged in del.icio.us, inbound links from a number of blog search engines, etc.

It will definitely improve your productivity and makes it even easier to track the content you like. For example, you can get only the good articles or the best ones of a blog or site via RSS, it depends on your decision.

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  • Use tags!

Tags are one of the most important features of web 2.0. Tags help you how to find content absolutely relevant to your needs. If you want to track your field of interest like this, try del.icio.us. If you’re a scientist or a physician, then your site is Connotea. Connotea can quickly save and organize links to your references, moreover you can follow the new additions to a tag by RSS. Here is the example: follow the best/selected articles about medicine 2.0.

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  • BioWizard.com:

I know BioWizard should be in the category of 3rd-party PubMed tools, but I think this service is much more than that. It keeps you up-to-date with the most important published literature as chosen by the global biomedical research community. How does it work?

BioWizard users submit relevant, timely research articles they have found to be useful and interesting. The articles you submit are then read by the rest of the community who promote articles they feel are deserving of recognition. The best articles in a research field are brought to the top page for all to read and discuss.

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Through Biowizard, not just you can track all the papers writing in the field of yours, but you can get the best articles (selected by the scientific community) via e-mail.

  • Google Alert:

If none of these work for you, or you’d prefer an even simplier method, then use Google Alert. It will bring all the recent articles/blogposts to you, all the new results for your search term. Personally, I follow the term personalized medicine via this free service to know about all the new articles written on this topic.

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As it’s so important to be up-to-date in your field, use these simple, free and comfortable methods to track the information you need. If you happen to know more tools/services, don’t hesitate to leave a comment for us.

Related links:

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