Caitlin Smith has a B.A. in biology from Reed College, a Ph.D. in neuroscience from Yale University, and completed postdoctoral work at the Vollum Institute.
Have you been hearing “There’s an app for that!” more often inside the lab than out? If so, it’s for good reason. The number of apps for smartphones and tablets is increasing exponentially, as these devices become smarter and increasingly ubiquitous in researchers’ lives. Useful new apps are popping up continually—here’s a brief scan of some new apps from 2015, and how they are assisting scientists to get through their daily research challenges.
Smoothing the workflow
Reinhard Baumfalk, vice president of R&D in instrumentation and control at Sartorius Lab Instruments, says customers are becoming more discerning when it comes to apps. “The ‘hype’ about apps in general is over,” says Baumfalk. “Now customers have a close look at the ‘added value’ [and] clearly appreciate if an app makes their daily life more efficient and convenient.” Sartorius’ newer apps include functions such as data analysis and remote control of lab instruments. For example, the Biostat A app (for iOS and Android) supports the company’s Lab-Bioreactor Biostat A instrument.
Other vendors also are releasing apps that enhance the use of particular instruments, such as Thermo Fisher Scientific’s NanoDrop User app for iPad. This app lets users view and analyze data from their NanoDrop 2000/2000c spectrophotometers, including comparing absorption curves and overlaying data files from multiple experiments.
As mobile apps have become more common in research labs, developers have found that the apps that attract and keep users typically “provide contextual information and functionality at the moment users find it most useful or applicable to their work,” says Tricia DiPiazza, mobile applications developer at Promega. Making workflows faster and easier is paramount, she says, which is why convenience-tool apps are so popular. The free Promega Protocols and Colony Counter apps are two recent examples (both for iPhone and iPad).
Promega developed its Protocols app in response to customer requests to run protocols on mobile devices, including in areas such as PCR, cloning and protein purification. “It allows users to [check] off steps as they’re completed, set timers and make annotations to protocol steps during a run,” says DiPiazza. “Customers can edit Promega’s protocols or create their own custom protocols from scratch.” The Colony Counter app counts colonies on agar plates automatically upon snapping a picture of each plate. It enables the user to refine counts by manually selecting colonies or removing false positives, as needed.
Abcam’s own app (for iPad/iPhone) also offers many types of protocols, including for flow cytometry, Western blotting and immunohistochemistry, though these cannot be edited. In addition, this app offers tools handy at the bench, such as buffer recipes, a dilution calculator and a timer.
Keeping track of it all
Mobile devices have become instrumental in helping busy people keep track of things—and the lab is no exception. BioData’s Labguru has differently geared apps for the iPad and smartphones, both of which help researchers to keep tabs on protocols and lab reagents. The iPad app is dedicated to protocols, and it’s meant to sit on the bench with you as you work, so you can check off steps as you go. The smartphone app (for iPhone and Android) keeps track of lab inventory, showing precisely where to find items in the lab. “It lets users virtually peer into an individual box and peruse each tube inside—not just its position, but also details about the tube’s contents and history,” says Xavier Armand, senior product specialist and creative director at BioData.
A new feature in the company’s iPhone app takes advantage of the built-in camera, such that photos can be linked from your iPhone to your research project. Labguru apps include many other features, but Armand says a customer favorite is the timer for protocols. This “gives users the ability to run a protocol step and set a time that triggers an SMS [text message] when complete,” he says—which lets you grab lunch without missing a step.
A plethora of apps is available for reference material, molecular structure, graphing and calculations. Some examples include StateCalc HD (for iPad/iPhone, $1.99), a thermodynamic calculator that provides a chemical’s physical state given the entered parameters. Other information-packed chemistry reference apps include ChemTrix Chemistry Calculator (for iPad/iPhone, $3.99), The Chemical Touch (for iPad/iPhone, $0.99) and Chemical Engineering AppSuite HD (for iPad/iPhone, $0.99). With too many handy features to describe in detail, these apps calculate chemical formulae and molar mass of compounds, provide easy access to the Periodic Table and include many types of calculators (e.g., mass, temperature, conductivity, kinematic viscosity, specific heat capacity). The Quick Periodic Table of the Elements app (free for iPad/iPhone) lets you color-code the Periodic Table in different ways, depending on your interests, so it’s easier to find the information that’s relevant to you.
Two newer math apps include Statistical Free (free for iPad/iPhone) and TouchPlot (for iPhone, $0.99). Statistical Free calculates mean, median, variance and standard deviation for entered data sets, and it provides multiple types of graphs, along with Z-scores. TouchPlot enables you to plot up to three functions on one graph and gives information such as the zero point, minimum, maximum, intersection points and integrated regions of curves.
Apps are great for viewing 3D molecular models, because the ability to rotate and zoom using hand gestures is so convenient and intuitive. With the Ball & Stick app (free for iPad/iPhone), you can download protein structures from the RCSB Protein Data Bank and display them in various ways (including, but not limited to, ball-and-stick models). ChemDoodle Mobile (free for iPad/iPhone and Android) works with commercial desktop software ChemDoodle, but the app can be used without owning that software. It lets you draw a chemical structure and then creates a 3D version of your molecule that you can view, rotate and analyze. It also gives molecular characteristics such as formula, mass and predicted nuclear magnetic resonance (NMR) spectra.
Genomics and proteomics
With the recent explosion of genomics and proteomics research, mobile apps for these areas are beginning to emerge. Integrative Genomics Viewer (free for iPad) from the Broad Institute lets you view genomic data files at different levels by zooming in and out. The app iCOPs (free for iPad), whose name stands for intuitive cardiac organelle protein atlas, uses the online proteomics resource Cardiac Organellar Protein Atlas Knowledgebase (COPaKB). The app lets you analyze raw proteomics data and search the COPaKB for relevant keywords. The BioCyc Pathway/Genome Databases app (free for iPad/iPhone) lets you browse BioCyc, which comprises almost 5,500 pathway/genome databases, for information such as genes, sequences and pathway diagrams. BioGene (free for iPad/iPhone) lets you search gene names or symbols using Entrez Gene at the NCBI, for information on the gene and its known functions. It includes a handy summary of research papers on the gene, with PubMed links to their abstracts.
DNAApp is a new Android app for analyzing DNA-sequencing data on smartphones. The app lets you open and read the ab1 files generated by sequencers and see the chromatogram, “something that previously could not be performed easily on phones,” says Samuel Gan, assistant principal investigator in the Bioinformatics Institute (BII), a research institute under Singapore’s Agency for Science, Technology and Research (A*STAR). To prevent DNAApp from getting too big, peripheral apps are available to add specific features modularly, as needed. The benefit of being able to do a quick preliminary analysis via smartphone is “fast detection of mutations or unexpected issues in the sequencing data,” says Gan.
As apps have become intuitive, second-nature sources of information for scientists in their personal lives, it’s only natural that researchers reach for them at work, too. With the recent release of the Apple Watch, it remains to be seen whether smartwatches will join smartphones and tablets as research tools—but smart technology is definitely in the lab to stay.