Posted by: shrikantmantri | December 3, 2009

BioKM: Cloud-based Research Knowledge Management [NGS]

via Next Generation Science by on 12/1/09

BioKM is a new way to keep research knowledge organized. An internet-based service, BioKM is designed to meet the everyday needs of researchers in an academic lab environment, allowing them to store, search, share and manage laboratory and research data.


BioKM provides a number of tools that enable users to plan and track research projects, organize materials and maintain a knowledgebase. To promote communication and discussion, users are able to exchange comments in all areas of BioKM. I asked Jonathan Gross, founder of BioKM, if NGS could get a closer look at the service and he was happy to set us up with an account. Read on for the review and a special offer for NGS readers.

The BioKM home page

The BioKM home page is organized with a row of tabs across the top that access different sections of the site: the Home page, Projects, Biocollection, Materials, Knowledgebase and Molecular. Above the tabs on every page? are links for help and account management as well as a search box. The home page provides an overview of recent activities in the lab and includes a weekly calendar, project updates, knowledge updates, messages and tasks.

When you add an event to the calendar, you have the option of keeping it private or sharing it (with everyone or select members). Unfortunately, there doesn’t appear to be any method for notification of events; email notifications would be great. Additionally, the calendar can’t be subscribed to in an external application such as iCal or Google Calendar. Tasks also appear in the calendar. Tasks can be added from the home page or from individual Project pages (below).


[ back up to the BioKM home page ? ]


The Projects tab opens up the projects module, which allows users to describe their projects, including all relevant steps or milestones, experiments and results. The list of projects can be filtered by member.


To create a new project, you simply click on “New Project”, add a title and optional description, set the start date and project owner, and indicate who can view the project. Once a new project has been created, the project page allows you to add milestones, link resources, events or tasks, and upload files or images. There’s even a section for other users to comment on the project. Additionally, at top there’s a notes tab that allows you to add notes for each project. Very useful for supplementing your lab notebook or adding ideas while working on the website.


In case you’re concerned about BioKM data security and safety, all communication is encrypted and all data is automatically backed up daily to a remote server.
[ back up to the BioKM home page ? ]


The Biocollection tab opens up the collection module, which is designed to help you update, search and manage your biological collection. There are separate tabs for bacteria, fungi, yeasts, seeds, plants, flies and cell lines. Some of the collection types even have default characteristics, but I wasn’t able to make much sense of them. For example, when I chose the collection type “Bacteria”, there was a list of default characteristics: name, strain, sensitivity and description. However, below the list of default characteristics was an input box simply labeled “Characteristic” and a button that allowed me to add additional characteristics. So there really isn’t a set of defaults — rather, it’s a list of suggested characteristics.

At the top of the page for each collection type tab is a search box that allows you to search the specific collection. Several of the collection types offer advanced search functions.

One thing I was surprised with was that “Human” and “Mouse” weren’t on the list. It would be nice if BioKM would simply offer an “other” option, allowing users to create their own biological collections.
[ back up to the BioKM home page ? ]


The Materials tab opens the materials module, which aids in keeping track of all the materials in your lab. You can describe any material or equipment used in the laboratory, keep track of ordering and delivery, and manage companies and storage locations. At the top of the page is a search box that allows you to find material by typing the name, catalog number or material description; advanced search functions are also available. From the Materials tab main page, clicking on the green basket icon at the far right side of the item row takes you to a page where you can add the item to your cart. You can also add items to your cart directly from individual material pages. This is a pretty cool feature, but I don’t know how well it works since I wasn’t able to actually submit orders.


The Storage tab in the materials module at the far right side of the row allows you define storage spaces in your lab. As materials are entered into the system, users can designate a storage location, which cross references materials with storage locations. There’s also tabs for boxes and tubes, allowing you to create boxes and define tubes and storage locations.


[ back up to the BioKM home page ? ]


The Knowledgebase tab opens up the knowledgebase module, the place where lab knowledge is shared. There are three tabs for the knowledgebase module, one for papers, one for protocols and one for documents. At the top of the page for each tab is a search box that allows you to search the specific knowledgebase; papers and documents offer advanced search functions.

The Papers tab integrates a PubMed search feature. I was impressed with this feature as it made it incredibly easy to add a paper to the knowledgebase. Once a paper is added, you can add tags and link to other resources, files (like the PDF) and/or images. Users can also leave comments.

You can also import papers from EndNote using an EndNote XML file. It would be nice if this feature could be expanded to other reference management platforms.
[ back up to the BioKM home page ? ]


The Molecular tab opens the molecular module where you catalog all of your lab’s molecular entities. There are individual tabs for genes, primers, plasmids, antibodies and nucleic acids. This is a much better system than a spreadsheet shared by everyone in the lab! At the top of the page for each tab is a search box that allows you to search the specific molecular entity; the plasmids tab offers advanced search functions.
[ back up to the BioKM home page ? ]


Overall, I was impressed with the BioKM system. As someone who, back in the late 1990s, designed and built a website for the lab I did my graduate work in, BioKM is a giant leap into the 21st century. The website runs relatively fast, thanks to the minimalist design of each page. I especially liked the “Recently Viewed” box that appeared on every page, making it easy to navigate to previous pages.

The one thing I didn’t like about the BioKM website was the tabbed navigation. Specifically, when you entered a module, all the other tabs disappeared, making it impossible to navigate from one module to another without first visiting the home page. A simple drop down menu when hovering over the home tab could easily solve this navigation issue.

The other thing I was disappointed with was that the site’s search engine didn’t offer advanced features: it would be useful to have the ability to restrict searches to one or more modules and/or perform complex queries. Note that within a module, you are able to search that specific module. Nevertheless, the site-wide search engine could be more robust.

There are five plans available: Free, Small, Basic, Premium and Max. The Free plan allows for 10 users, 20 managed projects and 50 MB of storage space. Each of the other plans provide support for additional users, active managed projects and storage space; prices range from $70 — $320 per month. For Small and Basic plans, the plans average out to $7.00 per user per month, providing 200 — 250MB of storage space and 4 — 5 active projects for each user. Quite reasonable.

Special offer: for NGS readers, BioKM is offering an extended trial period (60 days instead of just 30) and 10% off any of the paid plans. Look over the BioKM plans and pricing, click on the “Sign up” button for the plan you’re interested in and enter “NGS” without quotes in the discount code box.

BioKM is on Twitter @BioKM. Additionally, there’s also a BioData Product Blog that posts industry news, features research and offers BioKM tips and updates.

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This article was published on Next Generation Science.

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