Labfolder integrates Medeley in its digital notebook app

Screen Shot 2014-03-11 at 7.39.46 AMLabfolder officially announces the integration of Mendeley to its features. Mendeley is one of the largest international research networks and reference manager solution. With Mendeley’s integration in labfolder, users can now include references from their Mendeley library directly in their digital lab notebook. They can also add links to pdfs. Conversely, pages from Labfolder notebook can be exported to Mendeley as unpublished work.

Labfolder released mobile app

labfolder_logo_02_no_tagline_2083x500Labfolder is a cloud based digital lab notebook where users can write, draw and put together reports of their latest experiments (see blog post). They recently announced the released a mobile version of the service..

Users can now directly access their data on the go. They can also record their experiment in the lab using their mobile device, annotate them and store them in the cloud. The app is available for Android and AppStore.

Labfolder: a digital lab notebook

Screen Shot 2013-11-21 at 10.45.41 PMLabfolder is an online digital lab notebook. An online space where users can write, draw and assemble reports of their latest experiments, that they can then safely store in the cloud.

The digital lab notebook revolution has been announced for quite some time now. There are promises of digital notebooks accessible from anywhere that are data rich, searchable, sharable and never lost or damaged by spilled coffee.  But the path toward its full implementation in academic labs is long, partially because no alternatives really beats the old notebook and pencil when it comes to user friendliness. So in that respect, the challenges faced by Labfolder are significant.  But Labfolder proposes interesting functionalities and a nice, clean, fresh interface that may seduces more than one researcher.

The Labfolder experience start by creating a new folder (what a surprise) in your project tab. Under each folder, multiple entries can be added, corresponding to the pages of your traditional lab notebook. Within each entry, the users can create boxes containing text, images, links to files and hand-drawn (or should I say mouse drawn) sketches that can be useful to annotate images. These boxes can be easily resized or moved around and when satisfied with an arrangement, the entries can be saved and reused as templates. After the content is added, the final entries can then be save to the cloud, or downloaded as a pdf for sharing.

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Labfolder is completely free for individual use and for groups up to 3 users. A cloud space of 3 GB is offered to store all files. Forming a groups with other Labfolder users enables sharing entries and templates with collaborators.

Labfolder was started by two german PhD students from the MaxPlank Institute; Simon Bungers and Florian Hauer. They where surprised how digital tools were poorly used in research and decided to add their contribution by founding Labfolder. Labfolder is an ongoing venture, and encourage users to send their comments and ideas to them (contact@labfolder.net).

Design and share DNA sequences with Benchling

Screen Shot 2013-10-17 at 10.16.30 PMCollaboration seems to have never been easier with the collection of online tools at our disposal. These tools take advantage of the cloud to store data accessible everywhere to anyone. The software is usually browser-based, which makes access simple and fast. As mentioned here several time before, online tools aiming at enhancing collaboration between researchers have flourished over the past few years (see GitHub, Authorea or SciGit for example). Benchling has been named the GitHub for genetics, with it, anyone working with DNA can effortlessly design, analyze, and share sequence data. Benchling gathers into one platform most of the tools you will need to manipulate genetic sequences. Getting ready for cloning? Benchling will help you in the process with tools that identify restriction sites, suggests appropriate reaction buffers and can generate virtual gels to compare theoretical to experimental reaction products. Other bioinformatic tools offered by Benchling help you design primers, align multiple sequences or annotate sequences. The fruits of your hard work can then be tagged and store in the cloud, in an easily searchable format. Benchling also generates interactive sequence for easy visualization of constructs.

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The workspace can be divided into the sequence and the plasmid map. All most items are interactive. To the far right, tools to align sequences, annotate, design primers and more.

Benchling is also about collaboration. Users can grant access to their sequence libraries for download or editing by collaborators. Changes in the sequences can be tracked with the possibility to revert to a previous version. All the data is stored in one location, meaning no more exchanging emails that get lost or overlooked. Benchling was founded in August 2012, by Cory Li and Sajith Wickramasekara.

Lab techniques, protocols, tips and tricks on camera with Benchfly

2013-07-26-benchflyA large number of landmark scientific studies are hard to reproduce by independent labs. The reasons are numerous, but  incomplete and imprecise protocols are often to blame. Indeed the protocols published in most journals miss essential details such as the “little tricks” that make experiments work. Over the past few years, various initiatives have been launched to address the problem, and video protocols seem to stand out as one of the solutions.  If well produced, video protocols can be captivating and help to quickly grasp protocols or techniques in detail.

Benchfly is a central location to view and share videos of laboratory protocols, tips, tricks and techniques. It hosts short videos of virtually anything that can be useful to experimental scientist in the field of biology, biochemistry and chemistry.  Anyone with a camera-equipped smartphone is invited to create videos of their own experiments to share with the world. Benchfly made it easy for anyone to add, edit and share videos through their platform. And since making scientific expertise free and accessible to all is part of Benchfly’s core values, the videos are open access with no need to sign-up to view. Recently Benchfly also went live with a mobile app for both androids and iPhones so that filming and watching the videos is easier while in lab.

Since videos have become an essential tool for marketing and public relations purposes, Benchfly can also partner with companies, to produce, host and disseminate science-based videos. On top of this, Benchfly also hosts a more social component, with a great blog with tips and stories about the struggles and joys of being a researcher. Benchfly has been around for a little while now, created in 2009 by Alan Marnett in Cambridge MA USA.

Share and access rare samples with Sample of Science

Screen Shot 2013-08-05 at 10.34.57 PMSample of Science is a new web-platform designed to promote collaboration between scientists by stimulating the dissemination of scientific samples.

Dr. Romain Melet, co-founder of Sample of Science explains:  “the advancement of science highly depends on how efficiently the scientific knowledge circulates among scientists being located in geographically distant laboratories and working in different fields of research. Since a significant part of published results relies on highly specific research samples, such samples need to be considered as an integral part of scientific knowledge. Therefore the circulation of samples between scientists needs to be promoted.

That is where Sample of Science comes into play. The website is an exchange market for samples, with a focus on material science (although the platform will be opened to other fields in the future). Unique materials such as microporous polymers and luminescent gold nanorods are currently listed on the website. This system allows scientists creating new materials to make the most out of their research efforts, while sample adopters do not waste resources in the synthesis of already existing samples.

Sample descriptions are published on Sample of Science Bulletin, a peer-reviewed open access journal, thereby providing a citable reference and a Digital Object Identifier (DOI) to each transferable samples. The “sample author” and a “sample adopter” can use the platform to discuss about the opportunity of transferring a sample. Sample transfers are then published on Sample of Science Bulletin, making any exchange publicly trackable.

This is a great example of how online tools can favor more collaborative and international research efforts. Often collaborations are started between researchers with a new materials or tools and researchers with a new questions to answer. Sample of Science with an easy to use and centralized platform should help formalize these interactions and promote new collaborations.

The American Chemical Society releases their ChemWorx research management tool

The American Chemical Society recently released a new online research management tool: ACSChemWorx Totally free, it allows you to upload your favorite pdf to the cloud and synch them between your devices. It also includes features to streamline publishing in ACS journals. The tool seems rather mature. Have a look at the features announced by ACS:

  • Import, manage and search your existing reference library
  • Store, markup and highlight PDF documents
  • Share your reference library and files with collaborators
  • Manage research activities via groups, projects, tasks, calendars, and events
  • Cite references without leaving MS Word or LaTeX
  • Track citations to any of your published articles