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Practical Apps for a new lab

Note: This post was written by Scott T. Aoki, Assistant Professor, Dept. of Biochemistry and Molecular Biology, Indiana University School of Medicine, and Kenneth A. Matreyek, Assistant Professor, Dept. of Pathology, Case Western Reserve University School of Medicine

Let’s start with an obvious statement: starting a new research lab is challenging. We all know that coming into the position, but the realization quickly hits us that a great deal of the challenge comes from our lack of experience running a small business. This responsibility includes managing people, balancing a budget, and keeping track of our scientific results and laboratory inventory.  The science is the easy part of the job.

Unlike many of our mentors, we are starting our labs in a digital age. File cabinets and shelving just take up space. We care more about computational storage and processing power. This mindset also influences how we want to organize our labs and communicate with our lab members. We have now experienced this conundrum firsthand. Here is a list of considerations we confronted when choosing software for our new labs:

  1. Many Universities and Institutes purchase software subscriptions for their investigators, staff and students. While some of these programs are fantastic, the yearly cost is often too big of an investment for those labs that need to pay out of pocket. We have found that there exist free alternatives one can and should try before taking out your credit cards.
  1. The preference between Mac versus PC (versus Linux) platforms is as contentious as our political affiliations. Choosing certain Apps may force a lab to use a specific platform and prevent the use of lab members’ personal electronic devices. An easy solution to this problem is to use web browser-based Apps.  Not only does this allow the use of different operating systems, but it also allows seamless access from multiple computers including those located outside of the lab.
  1. Software comes and goes in popularity and practicality, but chances are high that you will want the information stored in these Apps for years to decades. We shall not provide names, but some Apps are designed and use extensions that cannot be accessed by other software. In other words, removal of information from your current software may require you to manually copy the information to your new software.  This gigantic waste of time can be avoided with shrewd software selection.

With these considerations in mind, we present a small selection of free, web-based, adaptable Apps we use in our own labs. While this list may be outdated by the time you read this article, we hope it provides a starting point for you to find your own best solution.

Apps for lab communication.

  1. Slack (slack.com): Slack allows communication between lab members and stores that communication for years to come. Send messages and post files to the entire group, sub-groups, or individuals. Slack can also interface with other popular Apps, like Google Calendar and GitHub. New investigators can also access valuable information from their peers by joining New PI Slack (www.newpislack.wordpress.com).
  2. Google Docs, Sheets, Calendar (google.com): Google Apps remain an easy way to exchange documents, create new spreadsheets and files, or share lab events like birthdays or meetings. Cloud-enabled synchronization of documents and spreadsheets across users is key to avoiding redundancies and conflicting versions of lab inventories and manuscript drafts. Many institutions have access to G Suite for education, enabling free unlimited storage.

Apps for lab inventory and finances.

  1. Wave (waveapps.com): Wave keeps track of your grant dollars, salaries, and lab expenditures. The App allows you to upload receipts for permanent storage and organize your spending the way you want.
  1. Airtable (airtable.com): Airtable provides a simple interface to share and edit tables of information. Its flexibility makes it a great App to keep track of inventory, protocols, plasmids, and other common lab lists.
  1. Benchling (benchling.com): Many labs rely heavily on molecular cloning of recombinant DNA constructs for their work, but keeping plasmid maps easily accessible, well-annotated, and sequences verified can be challenging. Benchling makes it easy for an entire lab to maintain a central plasmid repository using an intuitive web interface.

Apps for notekeeping.

  1. Evernote (www.evernote.com): Evernote can be used to keep simple notes, document drafts, protocols and outlines.
  1. RSpace (www.researchspace.com): There are multiple web-based lab notebooks available, but RSpace is one of the more adaptable Apps out there. It has unlimited storage space, integrates with other Apps (like Slack), and files can be shared between lab members.
  1. GitHub (github.com): As the scale of scientific data grows, it’s become increasingly important for scientists to maintain well documented and reproducible data analysis pipelines and software repositories. GitHub provides a free, convenient, and effective platform for collaborative, open-source data science.

What are your favorite Apps? What considerations and solutions have you discovered? We hope this opinion stimulates sharing of ideas how to use technology to run our labs efficiently.

 

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