Core Biomedical Research Software and Web 2.0 Tools

August 24, 2008 | by

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.

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

Highlight HEALTH runs 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

June 29, 2008 | by

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 Mesko 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

March 12, 2008 | by

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.

Searching for Health Information Online Dangerous

February 22, 2008 | by

Approximately eight million Americans search for health information online every day [1]. However, the information those health seekers are reading may not be very healthy at all. A new study by the Center for Medicine in the Public Interest recently reported that the information prominently displayed in search engine results was not only misleading and confusing, but dangerous for patients [2]. Case in point: using two safe and effective prescription medications (Crestor and Avandia) as an example, nearly 65% of the first three pages of Google search results came from sites that were biased or contained unverified information. Add to this the fact that most search engine users click on a result within the first three pages of search results [3] and people searching for health information online are likely to be viewing websites that aren’t credible or trustworthy.

Health Web 1.0, 2.0 and 3.0

February 21, 2008 | by

This article was written by Matthew Krajewski.

If Web 1.0 was about being told what the best information for you was (like the flat top 10 results on Yahoo! or Google), then Web 2.0 is about giving more control to the individual and inviting them to participate in the world of information.

Letting users start conversations or organizing information to the benefit of the end user are two outputs of the Web 2.0 evolution. So what is Web 3.0?

health-search.jpgAn article in ReadWriteWeb recently attempted to define Web 3.0, the semantic web based on personalization and recommendation. Web 3.0 may become quite adept at trying to algorithmically match you romantically, like a modern version of the 1950s board game Mystery Date, and some companies have already made significant headway in recommendation and personalization, such as Pandora and their music recommendation jukebox-like interface.

Will health ever benefit from the semantic web? Perhaps. Nothing is impossible, but it’s hard to imagine a computer will ever know how to deal with queries like:

“I hurt and don’t know why.”
“Why won’t my wound heal?”
“Should I be worried about menstrual bleeding during pregnancy?”

These questions deal with the core physical nature of human beings and the nuances and language to express physical experience is so wide that Web 3.0 may never build the right bridge.

However, Web 2.0 — with intelligent interaction flow — can make answering the afore mentioned questions much easier. By categorizing the scary wilds of the web for an end user, it makes searching that much smoother.

Kosmix, the creators of RightHealth, have created a categorization technology that simplifies the web. This categorization of information is important for online health search, where the nature of queries can be intensely personal.

Asking a person concerned about his/her health to plough through homogenous search results is just plain cruel. Categorize the information, build your interaction flow around that categorization, and you’ve already helped make the mystery of a health question easier to understand. Web 2.0 puts the user or the user’s needs at the center of the product, at least when it’s done right.

Being smart about categorization and interaction flow is more than just dressing up search results. Standard search results will require a user to determine for themselves what is a trustworthy source and what is plain spam. RightHealth treats the categorization of health information much like how an editorial health site would treat their articles: insuring results are relevant, trustworthy and of value to the end user.

The user interaction associated with these valuable results is just as important, exploiting the value of Web 2.0 sensibility in order to be smarter about how health searchers interact with information to better understand their health. In Health Web 2.0, the user is just as important as the information they are trying to access. Building those bridges correctly is the way to effectively evaluate the quality of a Health 2.0 website.

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 search resources are listed in the Highlight HEALTH Web Directory.