I bough an iPhone 4 three weeks ago. Instead of just a mobile phone, I think of it as a pocket computer that you can also make phone calls with. Since computational biology and biomarkers are an integral part of my daily life, I’ve been actively searching for and evaluating a number of life science apps for the iPhone. Even though I think that apps are a big step backwards in the evolution of the computer desktop — very few take advantage of the “always connected” nature of the iPhone and exist in isolation — mobile Safari only allows you to have 8 pages open at once. Apps that can handle Web page display increase that number. This is a lifesaver for me, since I routinely have all eight pages in Safari open at any given time.
Here’s 12 “must-have” iPhone apps that top my list for biomedical research.
1. PubMed On Tap
PubMed On Tap enables you to search PubMed and save abstracts and/or PDFs downloaded from the Web in your own personal and searchable library. In the settings, you can specify the option to indicate full text and free full text as shown in the figure. You can also configure an advanced search, specifying fields such as author, year, journal, PMID, etc and search mode (i.e. full text or free full text). The app also keeps a history of past searches. Search results, including those with PDFs), can be emailed as formatted text or a RIS tagged record, which can be easily imported into reference management applications like Bookends or EndNote. Importantly, the PubMed On Tap supports landscape view.
Verdict: well worth $2.99 (a “lite” version is available for free but limits you to 5 hits per search).
2. Mendeley Lite
Mendeley is software that indexes and organizes all of your PDF documents and research papers into your own personal digital library. It gathers document details from PDFs, allowing you to easily search, organize and cite. It also looks up PubMed, CrossRef, DOIs and other related document details automatically, importing papers quickly and easily from resources such as Google Scholar, ACM, IEEE and many more at the click of a button. Mendeley Lite for iPhone syncs with your Mendeley research collection, enabling you to carry your personal PDF library with you wherever you go. The app keeps your documents organized in just the same way as your online collection, with easy access to all your collections, recently added items and favorites. You can download PDFs from your library over wifi where it will remain available to read offline at any time. Mendeley Lite requires a free account with Mendeley Web. The app is free.
Verdict: no better way to keep your personal digital library with you on the go.
Use BioGene to quickly learn about gene function. BioGene allows you to use your iPhone to search by name or gene symbol, and retrieves information from Entrez Gene at the NCBI. A gene query returns data such as aliases, chromosome location and gene ID. Although the app doesn’t include OMIM, each gene record includes a link to OMIM, which opens in Safari. Each record includes a page that lists references, with links to the corresponding abstract that opens in the app. Unique to the list, BioGene includes a font size control in the lower right-hand corner of the screen. BioGene was produced with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center. The app is free.
Verdict: simple and fast resource to lookup gene function.
For more extensive gene information lookups, check out BioGPS. BioGPS is a gene portal hub created by Andrew Su (FriendFeed: asu) et al. at the Genomics Institute of the Novartis Research Foundation. The BioGPS iPhone app allows users to use their iPhone to quickly search for a gene of interest and then browse data on gene and protein function from a wide array of online databases. Although in my hands the Gene Identifiers section often returned an error, “We’re sorry, but the requested page could not be found.”, other sections appear to work much better. You can find information on literature, reagents, gene expression, exons, pathways, the Gene Wiki, Pathway Commons and WikiPathways. The app is free.
Verdict: a one-stop shop for gene information.
August 22, 2010 Update: A way to circumvent the error described above is to use the mobile web interface: http://biogps.gnf.org/m/ In my testing, everything worked as expected. An additional benefit is that you don’t lose your query when you open something else (unlike the BioGPS app). To add BioGPS to your iPhone home screen, navigate to the mobile link above, hit the “+” on the Safari navigation bar and press “Add to Home Screen”.
genomePad makes portable browsing of genomic data hosted on the University of California Santa Cruz genome browser website possible on the iPhone. It offers customizable searches and maps from genome assembly or specific chromosomal positions. The app provides for genome track zooming and chromosome repositioning with navigation buttons and sliding control. Specific tracks can be bookmarked or emailed. Very useful app. The app is free.
You can read more about genomePad over at the OpenHelix Blog, where Trey Lathe explores the app in depth.
Verdict: the only way to browse the genome on-the-go.
With the Nature.com app, you can search, browse, read and bookmark full text content from Nature and Nature News — how’s that for cool? — and search PubMed. Enhanced functionality is planned for the app later this year (hopefully they’ll include topic sections so you can browse in a more focused manner), and personal and institutional pricing options will be available. I’m not a fan of subscription journals, so I’ll likely re-evaluate my recommendation of the app once I know more.
Subject to customer feedback, NPG intends to roll out access to other Nature branded journals and publications available on nature.com, including Scientific American. The app is free but requires registration on Nature.com.
Verdict: full text content from Nature — a no-brainer.
7. PLoS Medicine
PLoS Medicine is the leading open-access medical journal, providing an innovative and influential venue for research and comment on the major challenges to human health worldwide. The journal specifically seeks to publish papers which have relevance across a range of settings and that address the major biological, social, environmental and political determinants of health. The PLoS Medicine app is divided into three tabbed sections: most recent articles, most viewed articles and search. Articles can be read in the app, either as text or in PDF form, or on the Web in Safari. You can also browse the PLoS Medicine archive by collection, subject or issue. The app allows you to read full text content, as well as bookmark and share via email. Clean, straightforward and to-the-point. Very useful. The app is free.
Verdict: a “must have” app to stay current with PLoS Medicine.
The New England Journal of Medicine (NEJM) app offers medical research findings, review articles and editorial opinions from the current issue. The app includes free — that’s right, for a limited time, subscriber-only content is free — access to recent articles that have been published online in the last seven days, including research, reviews, commentary, and case materials; images; weekly audio summaries and a selection of full-text audio reads of Clinical Practice articles; and a selection of four procedure videos from Videos in Clinical Medicine. The app is free.
Verdict: a “must have” app to stay current with the NEJM.
Medscape is a free resource for Physicians and researchers, offering medical journal articles, MEDLINE, medical news, major conference coverage and comprehensive drug information. The Medscape app provides access to 3500+ Medscape Clinical Reference articles and includes sections for reference, drug interactions, news and CME. I like how this app divides up a given therapeutic area into specific diseases and then sections the information into Clinical, Differential Diagnosis, Workup, Treatment, Medication, Follow-up and Background. An account on Medscape is required. The app is free.
Verdict: an obvious choice for medical news, conference coverage and drug info.
Although it’s not as stable as the other apps in this list, I like GeneIndex. It’s versatile and enables you to do a number of things. You can do a simple gene symbol search and get links to a varitey of different resources, all of which open in the app: PubMed, Google Scholar, CiteXplore, NCBI Gene, OMIM, COSMIC, Uniprot, KEGG … the list is quite long. Additionally, you can search by chromosome (very cool), by alias and by keyword. The app also has a list of journal Web pages, all of which also open in the app. Best of all: both the web links and journal resources can be customized via a simple text file. Lastly, you can search and store PDF journal articles for offline reading, although I’ll likely use PubMed On Tap or Mendeley Lite for that. GeneIndex is ad-supported (although I didn’t see any ads in my testing). An ad-free version (GeneIndexAF) is available for $0.99.
Verdict: versatile and expandable gene search.
The caBIO app provides an interface for iPhone users to search and browse all the data available in caBIO (Cancer Bioinformatics Infrastructure Objects data service), a resource for accessing biomedical annotations from curated data sources in an integrated view in support of knowledge discovery. The caBIO data service is part of the Cancer Biomedical Informatics Grid (caBIG) program at the National Cancer Institute (NCI).
Even though the app has a cancer focus (which is great if you study cancer), one of the things I especially like is that the app lists ontology and pathway associations for a given gene. Why don’t more apps do this? The app is free.
Verdict: quickly access ontology and pathway data while mobile.
12. SABiosciences Pathway Central
I’ve saved the best for last. In my opinion, this is the coolest app in the list. SABiosciences has taken their pathway study resource Pathway Central and turned it into an iPhone web app. Featuring 100 categorized pathways, it’s a breeze to search and browse pathway maps on the go.
This is a free web app, not a native iPhone app. Follow the instructions to set it up here.
Note: to add it to your iPhone home screen, after following the instructions above, navigate to the bookmark, hit the “+” on the Safari navigation bar and press “Add to Home Screen”.
Verdict: no better way to have pathways at your fingertips.
When it comes to the life sciences and biomedical research, there is indeed “an app for that”. I hope you find this round-up of what I consider to be the most useful iPhone offerings for the life sciences informative. Feel free to share your favorite life science and biomedical research apps in the comments below!
For more life science apps, check out Ricardo Vidal’s list on My Biotech Life.
Walter Jessen is a digital strategist, writer, web developer and data scientist. You can typically find him behind the screen something with an internet connection.