Taralyn Tan Ph.D. Curriculum Fellow Harvard Medical
Make your research run a little more smoothly with these apps.
Is there an app for that? If there is, you should check if it's in GEN's Best Science Apps first! Every month, we bring you a list of the best biotech- and biopharma-related apps we think you, GEN reader, would find useful and/or interesting. Here is our most recent list of Best Science Apps. Enjoy!
Four stars: Excellent
Three stars: Very Good
Two stars: Good
+ Strong points
– Weak points
+ Many plugins, easy to use
– Can’t browse plugins, can’t create account on app
Are you ready to navigate the genome? The BioGPS app (which nicely complements the corresponding web resource) allows users to search for gene information on the go. Users simply enter a gene name (symbol or accession number) into the search field to bring up information for that gene in any of the eight supported species. For a given gene, one can browse a gene expression profile across different tissues/cell types, a list of gene identifiers, and a link to the corresponding Wikipedia page. Users can add genes to a favorites list within the app for easy access. Beyond the basic gene information, the BioGPS app includes access to a number of “plugins” (corresponding to various genomics resources). Users can also search for specific plugins within the app and can similarly add them to a favorites list.
Statistics Visualizer ★★★
+ Notes section to complement simulations
Sometimes it’s easier to learn things by doing as opposed to simply reading about them. That’s the philosophy behind the Statistics Visualizer iPad app, which provides simulations to demonstrate a number of concepts in statistics. Through these simulations, users can explore and learn about different discrete probability distributions (Poisson, geometric, and negative binomial) and continuous probability distributions (normal, student’s t, chi-square, exponential, and Snedecor’s F). For each simulation, users can adjust parameters such as n, the p value, and the left and right bounds of the plot. Each topic also comes equipped with a complementary notes section that is very useful for people with little-to-no knowledge of statistics. If you find yourself wanting even more statistics, you can upgrade to the paid version of the app for additional topics.
+ A great deal of scientific content
– Poor genome browser, can’t access data in app
It should come as no surprise to all of you slang-savvy readers out there that the Jane-Ome Project provides scientific information about the medicinal uses of marijuana. This includes a genome browser for information collected as part of the cannabis genome project pioneered by Medicinal Genomics. (Disappointingly, however, the “access data” feature of the app does not actually allow one to access the sequencing data within the app. Rather, one must give his/her email address in order to be sent an email containing a link to access the data online.) Beyond the genome browser, the app contains a number of factoids related to medicinal marijuana and a newsfeed of related news stories. Finally, there is also a section of the app dedicated to scientific studies and articles.
+ Contains both theory and simulations
– Notes are very advanced, some simulations are glitchy
If you you looking for an interactive way to better understand concepts in physics such as how a mass-spring system, temperature system, or pendulum system behaves, look no further than iDynamic, a great app by NgM Software that teaches these (and other) concepts through the combined use of theory and simulation. The app is divided into modules, each corresponding to a topic such as those listed above. For each module there exists a theory section and a simulation section. Under the theory section, app users will find a text introduction to the concept, including relevant math equations. (Users be warned, though: you will encounter advanced mathematical concepts such as partial derivatives.) The other section of the app includes interactive simulations demonstrating the behavior of the systems. Users can adjust various physical parameters and observe how those parameters affect the system. The app comes with a base set of free modules and additional modules can be purchased.
+ Protocol feature, nice descriptions of products
– Very commercial in nature
On the surface, the Cytometry app by Invitrogen may seem like little more than a product catalog. While it certainly is product-centric, the app warrants inclusion in this column because of the particular organization of the product information into informational/educational categories and because of the built-in protocol features. The app is organized into different categories corresponding to various applications of flow cytometry, including immune-phenotyping, antibody labeling, cell viability, and phagocytosis. Within a given category, the available reagents for that specific type of experiment are given. In this way, researchers are able to get a sense of the types of analyses that are possible and the reagents that are available (albeit just from Life Technologies). Additionally, the complete labeling protocol is given for each reagent, complete with an interactive timer feature for each incubation step. Simply tapping the clock icon will start a timer corresponding to the correct amount of time.
+ Easy to use, includes citations
Just thinking about this app makes me feel sick to my stomach. Bad puns aside, the InDigestion app is an easy-to-use app that provides the sequences of peptides resulting from protein digestion. Users simply search for a protein to display information (such as molecular weight and isoelectric point) for that protein. The complete amino acid sequence for the protein is also provided. Using the “digest” feature, users can then digest the protein sequence with an enzyme of their choosing. They also have the option to specify other chemical modifications or digestion constraints such as minimum or maximum mass-to-charge ratios. The resulting peptide sequences are then displayed, along with a plot of mass-to-charge ratio versus relative intensity for the peptides.