Highlight HEALTH 2.0 Interview: Bertalan Mesko

In 2006, Bertalan Mesko (Berci) started Scienceroll, a blog about genetics and popular medicine. It quickly evolved into a leading source of information following the impact of Web 2.0 on medical education and healthcare. He posts regularly on Twitter (@Berci) about health 2.0, medicine 2.0 and personalized medicine (top five words: rt, ff, medicine, medical, health), and maintains two “microcarnivals” on FriendFeed: Gene Genie and Medicine 2.0.

Berci Tweet Cloud

Over the past four years, Berci has accomplished many things. In 2009, he started a Ph.D. in clinical genomics after graduating with an M.D. from the University of Debrecen in Hungary. From his work at Scienceroll, he has been invited to lecture on medicine in the Web 2.0 era at several clinics and departments at the University of Debrecen, and has presented at several medical conferences around the world.

Berci Mesko

In 2008, Berci launched the first university credit course for medical students that focuses on Web 2.0 and medicine (med20course.wordpress.com). He also founded Webicina.com, the world’s first medical Web 2.0 guidance service. Webicina aims to ease the work of physicians and scientists by recommending useful tools and sites and by presenting them the new world of Web 2.0. Just last week, Webicina launched its 65th medical topic spanning 15 languages on medicine.

I’ve known Berci Mesko since 2006 and we recently had a chance to talk about Scienceroll, Webicina and his professional path in the Web 2.0 era.

Highlight HEALTH 2.0 – Year in Review 2008

As Highlight HEALTH 2.0 celebrates its’ first year following the use of Web 2.0 in health and medicine, I would like to take this opportunity to thank you for your readership.

Three websites make up the Highlight HEALTH Network:

Each of these sites has a different purpose. Highlight HEALTH 2.0 is focused on new ideas in health and medicine (if you’re interested in writing a review about a social health network or co-blogging about the integration of Web 2.0 technologies into health and medicine, please let us know). Highlight HEALTH promotes advances in biomedical research to encourage health literacy. Lastly, the Highlight HEALTH Web Directory is an online reference guide for reliable health and medical information.

There are more ways than ever to connect with the Highlight HEALTH Network, including email/RSS, Twitter and Facebook. Highlight HEALTH 2.0 is also optimized for the mobile web.

If you enjoy the articles and reviews here at Highlight HEALTH 2.0, I’d like to ask for your continued support.

… and above all, please continue to read and participate.

Top 5 most popular articles

Here are the most popular articles for 2008 (top 5 based on the number of page views/number of days posted):

  1. Online Patient Community Battle for Survival: MDJunction
  2. iMedix: Reliable Health Search and Patient-to-patient Social Network
  3. Mednar Search … and Hope said, “It is good.”
  4. Following the Tweets of Health
  5. Core Biomedical Research Software and Web 2.0 Tools

Thank you and Best of Health in the coming year!

Core Biomedical Research Software and Web 2.0 Tools

Following a discussion on Twitter, Dr. Chris blogged about essential medical software and invited others to share their “core apps”. I thought I would add to the discussion with my own essential programs, albeit with a genomics/pre-clinical research bias. Since a number are Web 2.0 apps, I’m posting this on Highlight HEALTH 2.0.

First: a little about me. I’m a bioinformatician working in neuro-oncology.

Bioinformatician: an individual that uses information technology as applied to the life sciences, especially the technologies used for the collection, storage and retrieval of genomic data.

Last month, an article debating Scientist vs Developer in Bioinformatics was posted on Web 2.0 and Semantic Web for Bioinformaticians. I would fall into the first category (Scientist Bioinformatician), as I’m interested in testing hypotheses and discovering new knowledge.

Michael Barton wrote an entertaining article on career paths for Bioinformaticians earlier this year. In the World of Bioinformatics Quest, my character class is a Wet lab Bioinformatician (WB):

A dry lab scientist, working in wet lab, the WB is the support for all things computational biology in the laboratory. The WB is familiar enough with Perl to create simple scripts, but the real strength of the WB doesn’t lay in writing code, but rather in using tools. While most bioinformaticians are familiar, in theory, with how to find a gene of interest, the WB uses these tools day in and day out — the WB puts many to shame on basic bioinformatics. While others have their head in the clouds thinking about theories and algorithms, the WB is getting his hands dirty with real data as it is being produced.

The majority of my time is spent performing Functional and Comparative Genomics on DNA microarray data. The information I analyze is used to further our understanding of the molecular pathways altered in neurofibromatosis and to identify potential therapeutic targets.

Note that I’m an Apple user (MacBook 2.16 GHz Intel Core 2 Duo, 3 GB 667 Mhz DDR2 SDRAM), so all my core apps are for a Mac. With all of the visual data I manipulate, a good monitor is essential; I use a Samsung Syncmaster 245BW 24″ LCD monitor. Finishing out the hardware list is an Apple wireless keyboard and mouse.

Local Mac applications

GeneSpring GX

GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of gene expression data. Sure, there are more powerful alternatives (I hear all you R users grumbling …). Nevertheless, the ability to quickly manipulate gene lists and display gene expression patterns makes GeneSpring GX an essential core app for expression analysis.

R/Bioconductor

I use R in conjunction with Bioconductor, an open source and open development software project for the analysis and comprehension of genomic data, principally for data normalization prior to import and analysis in GeneSpring. I routinely use custom CDF ([Gene] Chip Definition File) libraries, so R/Bioconductor is absolutely essential for data preprocessing.

Microsoft Excel

Genomics analysis requires manipulation of many, many data points (100 samples x 56,000 probe sets = 5.6 million data points). Sorting, searching and organizing the data can all be accomplished with Microsoft Excel. A necessary evil.

Skim

Skim is a PDF reader and note-taker for OS X. It is designed to help you read and annotate scientific papers in PDF, but is also great for viewing any PDF file (think Preview on steroids). Unlike Adobe Acrobat, it’s FAST.

Bookends

I’ve tried a number of applications to organize and tag scientific journal articles. Keeping up is an impossible task. I’ve tried several applications (yes, I’ve even tried Papers). However, for those of us that write research articles for publication, a reference manager is an essential app. Bookends is bibliography software that can also organize PDFs. The interface isn’t flashy but it’s a powerful piece of software. You can perform PubMed searches, retrieve references and associated PFDs and create static, smart and virtual groups to organize and find information in your personal collection. And it’s FAST. Bookends uses Spotlight to search within PDFs. You can search titles, abstracts, authors, journals, dates and more. Bookends is actively supported and has a useful user forum.

Microsoft Word

Speaking of writing research articles for publication, Microsoft Word is another necessary evil. I’m writing all the time and a powerful word processor is a must.

Microsoft PowerPoint

Yes, another Microsoft app. Scientists are always talking about their research and pictures speak louder than words. Especially in my position as a Bioinformatician, I need software that allows me to display and present information; Microsoft PowerPoint is that application.

I should pause here and mention out that I’m testing Apple iWork to replace Word and PowerPoint. The entire Office suite isn’t optimized for OS X (it really runs poorly) and both Pages and Keynote — iWork apps — rival the utility of Word and PowerPoint.

Web applications/databases

I spend a great deal of time analyzing large high-throughput gene expression data sets. Each analysis involves addressing several hypotheses and establishing biological meaning from the data. I rely on a number of web applications and databases to identify genes or gene sets associated with a particular phenotype (meaning an observable characteristic) and to identify enriched biological themes, particularly gene ontology (GO) terms.

PubMed

Efficient literature search is essential to the practice of Evidence-Based Medicine and to Biomedical Research. PubMed provides free access to MEDLINE, one of the largest searchable databases of biomedical research articles. An absolute necessity.

DAVID Bioinformatics Resources 2008

The Database for Annotation, Visualization and Integrated Discovery (DAVID) 2008 provides a comprehensive set of functional annotation tools for researchers to understand biological meaning behind large list of genes. I’ve tried various other tools for functional annotation analysis, but I find DAVID the most comprehensive app on the web. DAVID is owned by the NIH and is under continuous development and improvement.

OMIM

OMIM (Online Mendelian Inheritance in Man) is a comprehensive and authoritative compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. I frequently link to OMIM for genes discussed on Highlight HEALTH.

iHop

No, not the restaurant. Information Hyperlinked over Proteins (iHop) provides the network of genes and proteins as a natural way of accessing the millions of abstracts in PubMed. By employing genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed becomes bound together into one navigable resource.

Web 2.0 tools

I’m using Web 2.0 tools more and more in my daily workflow. Many have become indispensable for organization and communication.

WordPress

Both Highlight HEALTH and Highlight HEALTH 2.0 run on WordPress. I’ve used WordPress for a couple of years now and (between plugins and hacks) it does everything I need it to do.

Delicious

I gave up trying to manage browser-based bookmarks some time ago. Delicious.com allows users to tag, save, manage and share web pages from a centralized source. The latest addition to my workflow is the use of the “toread” tag to find bookmarked articles of interest for later review (since emailing or saving links to the desktop is inefficient).

FreshReader

I use RSS frequently, not only for blogs of interest but also to keep up with biomedical journals (current issue table of contents RSS), PubMed searches (to keep up with the latest published research in my field of work), LinkedIn updates and news. I try not to depend on Google too much, although that can be difficult nowadays. For RSS, I use FreshReader, a web-based, server type RSS and Atom feed reader. Fed up with slow feed readers? FreshReader is FAST.

FriendFeed

FriendFeed is becoming an excellent social networking tool, since several rooms have been setup for life science researchers and programmers. In addition to being a social aggregator, FriendFeed has comment streams that allow you to contribute to the conversation. In many cases, entire discussions are held entirely on FriendFeed.

Twitter

Twitter is also becoming a useful tool to communicate with other doctors and researchers (most are also using FriendFeed as mentioned above). Twitter allows you to keep up with people that share similar interests.

If you use both both FriendFeed and Twitter, I’ve found a convenient tool. MySocialChatter.com brings FriendFeed and Twitter together in a single web page using frames and automatically refreshes every few minutes. It’s quite useful for keeping an eye on the conversation, is easy to read (compared to some desktop apps) and is non-disruptive.

… And the rest that I couldn’t live without

Other everyday applications that I couldn’t live without:

Quicksilver

Act without doing. If you use a Mac, Quicksilver is simply a must have.

Expose

Move over command-tab (that’s alt-tab for all you windows users), Expose is AWESOME.

Mail.app

Mail.app, my e-mail program of choice.

Safari

The web, Apple style. Safari with the Saft extension is my internet browser of choice. OS X optimized and FAST.

Journler

My digital notepad. Journler is a daily notebook and entry based information manager. Never again do I have to deal with miscellaneous text files scattered across my hard drive or random bits of text emailed to myself. That said however, I am looking into Evernote to supplement (and possibly replace) Journler.

iTunes

My iTunes plays mostly ambient, new age music. I frequently work with Groove Salad or Radio IO Ambient playing in the background.

Final thoughts

So, there you go. There’s many applications, but since I’m a bioinformatician that should come as no surprise. I think you’ll get a better idea of who I am and what I do from the software tools I use and rely on everyday. These are my core biomedical research apps.

Are you a physician or biomedical scientist? Is there software or Web 2.0 tools that you couldn’t live without? What are your core apps? Share in the comments below or write your own post and link back here.

Medicine 2.0 #27 – Communication is Key

Welcome to the twenty-seventh edition of Medicine 2.0, the bi-weekly blog carnival of the best posts pertaining to web 2.0 and medicine.

Medicine 2.0 is the science of maintaining and/or restoring human health through the study, diagnosis and treatment of patients utilizing web 2.0 internet-based services, including web-based community sites, blogs, wikis, social bookmarking, folksonomies (tagging) and Really Simple Syndication (RSS), to collaborate, exchange information and share knowledge. Physicians, nurses, medical students and health researchers who consume web media can actively participate in the creation and distribution of content, helping to customize information and technology for their own purposes.

Communication amongst and between healthcare professionals and healthcare consumers is a necessary element to improve health and is critical for the delivery of optimal medical outcomes.

This edition of Medicine 2.0 covers a wide array of posts with one thing in common — Communication.

Web 2.0 Tools and Slideshows

Medicine 2.0

Gunther Eysenbach’s Random Research Rants

Dr. Gunther Eysenbach presents an archiving system for Citing Blogs, Preserving Cited Webpages etc with WebCite.

Clinical Cases and Images

Do you Twitter? Dr. Ves Dimov offers A Doctor’s Opinion: Why I Started Microblogging on Twitter.

Scienceroll

23andMe presented a slideshow recently in Second Life in the latest session of the Scifoo Lives On series. Dr. Bertalan Meskó covers 23andMe in Second Life: LIVE.

Jay Parkinson+ MD + MPH

Dr. Jay Parkinson asks us to Look, posting a presentation from George Halvorson, CEO of Kaiser Permanente, about health reform.

Pharma 2.0

Bunny Ellerin writes about Within3 and the results of a survey at the American Society of Clinical Oncology (ASCO) conference. There’s no doubt that social media is Changing Physician Behavior.

Online Video

Gene Sherpas: Personalized Medicine and You

Dr. Steve Murphy writes about the upcoming second Helix Health CliniCast on genetic testing, genomic medicine and the science of accurate warfarin dosing, asking How’s that for Genomic Medicine by Press Release?

Digital Pathology Blog

The Digital Pathology Blog reports that Mayo Launches YouTube Channel with videos highlighting the latest research and treatment advances at Mayo Clinic.

WSJ Health Blog

The Wall Street Journal Health Blog discusses online doctor consults, announcing that The Doctor Will See You on the Webcam Now.

Information Tools and Tests

College@Home

Many of us might forget there’s other search tools out there besides Google. Laura Milligan provides a comprehensive list of 100 Useful Niche Search Engines You’ve Never Heard Of.

davidrothman.net

David Rothman posts An Evaluation of the Five Most Used Evidence Based Bedside Information Tools in Canadian Health Libraries, a recent study published in the journal Evidence Based Library and Information Practice.

Medgadget

Personalized Medical Search Engine: With Medgadget describes the inclusion of Medgadget in Scienceroll Search, a personalized medical search engine powered by Polymeta.com.

NursingDegree.Net

Jessica Merritt highlights a number of ways to use Google’s Personal Health Record (PHR), offering The Ultimate Guide to Google Health: 60+ Tips and Resources.

Canadian EMR

Digital records and privacy can be a mixed bag. Alan Brookstone reposts the media report UK Health Agency Loses 31,000 Patients Records.

Sharp Brains

Alvaro Fernandez writes about the Brain Age, Posit Science, and Brain Training Topics, reporting both good and bad news regarding the assessment and training of cognitive skills.

Microarray Blog

Albin Paul discusses the options for a Semantic Search Engine for PubMed — Microsoft Vs Yahoo Vs Google Vs Oracle in Semantic Web Search.

Tomographyblog

András Székely discusses TomographyBlogSearch in the Making, describing the SeekRadiology Project, a search engine for diagnostic imaging.

Doctor-patient Communication

Canadian Medicine

Graham Lanktree reviews a study of prepared patients and internet information, which finds that the Web Buoys Doctor-patient Communication.

Medical Economics

Gail Garfinkel Weiss writes how the shift from authority-based medicine to one of shared responsibility is playing out in the exam room in The New Doctor-patient Paradigm.

The iPhone

Dr Penna

Dr. Sreeram Penna provides a list of health care applications currently available for the iPhone in Mobile Medical Software for the Iphone 3g.

Efficient MD

Dr. Joshua Schwimmer also writes about potential applications on the iPhone for doctors in The New 3G iPhone, the App Store, and Doctors.

Conclusion

That concludes the 27th edition of Medicine 2.0. My thanks to everyone who submitted an article. You can find more information about the carnival as well as the hosting schedule and past editions at the Medicine 2.0 Website.

Have you written a blog post about web 2.0 and medicine? Submit it to the next edition of Medicine 2.0 using the carnival submission form.

Diabetes 2.0

This article was written by Matthew Krajewski.

March 25, 2008 will mark the American Diabetes Associations’ 20th annual American Diabetes Alert Day. As implied by “alert,” the day serves as a call to action for those individuals at risk to take the Association’s Diabetes Risk Test, and make an appointment with a healthcare provider if necessary.

Since 54 million Americans have pre-diabetes, it is crucial for those at risk to take heed from the American Diabetes Association’s Diabetes Alert Day. Those at risk include overweight individuals, those not leading an active lifestyle (not taking enough exercise), and those with a family history of diabetes. Furthermore, the American Diabetes Association recommends that people aged 45 and older be screened every three years (those at higher risk should seek screenings more regularly).

Since diabetes has no cure, affects nearly 20 million Americans (of these 6 million don’t know they have diabetes), and is the fifth leading cause of death by disease, the fear of testing positive for diabetes and the seemingly insurmountable lifestyle changes and health management requirements accompanying the disease can be quite daunting. Fortunately, the Web provides a wealth of information, and the interaction developments offered by Web 2.0 can make the quality of life of those living with diabetes a little better. With 5 — 10% of all Web searches being health related, the need for people to not only get health information, but also make it easy to access and interact with, is vital and reflects the evolving needs of Web users that Web 2.0 seeks to meet effectively.

searching-for-diabetes.jpgSites like RightHealth.com, Healia.com, Revolution Health or WebMD are excellent starting points to quickly get acquainted with the information surrounding the topic diabetes. Healia provides multi-dimensional filtered search results, whereas RightHealth algorithmically orders information from across the web and presents it in an easy-to-understand content format. Revolution Health, Web MD and RightHealth all blend the lines of information and community to offer multiple dimensions to getting information on diabetes.

From RightHealth, I learned a bulk of the facts I already mentioned in this posting, as well as what diabetes actually is: a life-long disease characterized by high blood sugar levels. The causes of diabetes can include too little insulin (the hormone the pancreas produces to manage blood sugar), a resistance to insulin, or a combination of both. Beyond this basic information, RightHealth also features easy-to-understand jump-offs to other sites, like Trusted Sources (organizations connected with diabetes that provide detailed information about the disease), and an Explore section that gives a snapshot of the language and topics used to understand diabetes.

So Health 2.0 makes getting or understanding information about dense topics easier, but that’s just the beginning. A new site, Mamaherb.com bills itself as a way ” … to find natural treatments that can really help,” by fostering a community where users share stories about what alternative treatment options have worked for them. For diabetes sufferers that want to explore homeopathic remedies, Mamaherb is an invaluable resource. A search on “diabetes” showed that people had moderate success with such natural remedies as bilberry juice, buckwheat tea, broccoli extract and buchu leaves. Where else could you get this type of deep information easily?

The key to better health for diabetics is better control over the disease by carefully monitoring their blood sugar levels. This might sound simple, but it can be surprisingly complex. Fortunately, there is Sugarstats.com, which provides an interface to, “track, monitor, and share [your] blood sugar levels and other key statistics to help manage your diabetes online.” With timelines and graphs, it becomes easier and more accessible for a diabetic to manage the trends in their blood sugar levels and target ways to reduce blood sugar levels.

The touchstone of Web 2.0 is the user. While there are the mega sites like Facebook and MySpace where one could find other diabetics to share stories and advice, there are also even more targeted community sites which serve specifically the health or diabetic communities. iMedix.com is a place where users can rate medical articles that have helped them (like Digg meets Health) and chat with other people that share similar interests. When I searched iMedix for “diabetes,” I was told that there were three people online who I could chat with and around 500 offline that also share an interest and want to talk about diabetes. Another valuable resource was icyou.com, where users post health videos, which was a great way to cut through non-health-related videos you might find on mega sites like YouTube.com. But perhaps the most valuable resource was tudiabetes.com, which is a rich and vibrant community site committed to those afflicted with or touched by diabetes.

With such resources available today with the advent of Health 2.0, and by extension Diabetes 2.0, living life with diabetes just got a little bit easier.

About the author: Matthew Krajewski is a writer for The Kosmix RightHealth Blog, which uses information obtained through the RightHealth search engine to provide insightful posts about health-related news and issues.

Additional Health 2.0, Patient Social Networks and Diabetes resources are listed in the Highlight HEALTH Web Directory.