Chapter 7. Synbiota: An Entry-Level ELN for the Budding Scientist

Oliver Medvedik

Although promises of a paperless office may not have materialized yet, a bumper crop of ELNs (electronic laboratory notebooks) have been making the rounds to ease the gathering, processing, and dissemination of data. As we are constantly being reminded, without proper management, this torrent of data will soon overwhelm the scientific community with data anarchy, grinding progress to a halt and heralding in yet another Dark Age. Perhaps not, but the efficient management of projects when you have multiple students working on a summer iGEM (international genetically engineering machines team) becomes an absolute necessity, or things can quickly spiral out of control.

ELNs range from feature-laden systems that not only help you gather data and manage projects but, with accounting and inventory features, can essentially help you to manage an entire lab, to more basic systems that focus on individual and small group projects. Though still in beta mode, Synbiota is in the latter category and proves to be a good entry-level electronic lab notebook that allows those unfamiliar with this format of data recording and sharing to hit the ground running.

It comes packaged with a simple-to-use open source DNA annotation program, GENtle 2.0 beta, to help assemble your newly designed constructs. After uploading your sequence file, annotation is performed through a series of straightforward dropdown menus. The most useful functions, such as restriction digest mapping, are already preloaded. Files can then either be exported in a variety of formats, such as FASTA, or saved within the Synbiota.ca server for your teammates to see.

Synbiota has several registration options. In the free plan, you can have one collaborator share a notebook and have an unlimited number of public projects ongoing that can be viewed by anyone accessing Synbiota, along with one private project that only you and your teammate will have access to. All options also give users unlimited use of the open source DNA annotation tool, GENtle 2.0. Higher levels of access operate on a sliding payment scale, allowing up to 15 additional collaborators and 5 private projects.

According to Katty Wu, a rising senior at Stuyvesant High School who is currently using the site during a summer research project here at our community biotech lab, Genspace:

…Synbiota has been a very user-friendly tool to help organize the team's lab notebook. It's simple to use and the sidebar is a great way to navigate through all our entries. It has allowed me to easily communicate a day's work at lab with my mentors and lab colleagues…The service is extremely friendly and really values my opinions and problems. It's a site which allows starting research scientists, as well as experienced ones, to cooperate on an online environment knowing that someone's always got their back.

The site is still in beta mode, so bugs are to be expected, and new features can be added, such as a calendar to keep track of projects. I’ve emailed these and other suggestions to Connor Dickie (), cofounder and CEO of Synbiota, Inc. Throughout this summer, our students have had very fast and positive responses from Connor and his development team, Justin Pahara and Kevin Chen.

Currently, where Synbiota stands out is in allowing groups of students, scientists, and engineers to quickly get started using an ELN for data sharing. Uploading data is made easy through a minimalist interface that breaks everything down into four categories: Notes, Experiments, Protocols, and Literature. Having mentored four IGEM teams, I can attest to the difficulties in having students share lab notes with one another when they may be operating on different schedules. Having the information online just makes so much sense. Using a system such as Synbiota also expedites uploading of content to other sites, such as in a competition, or for eventual publication. In the end, you will have to transcribe your notebook into an electronic format anyway, so this is a great way to start getting used to the process. It also readily permits mentors to check on progress. So if you’re either new to the world of ELNs or if you have a boisterous team of students to manage on a cloning project, I would definitely recommend that you give Synbiota a shot. You can register for free at http://www.synbiota.ca.