All the workloads have been tested with Cloudera Distribution of Hadoop 3 update 4 (CDH3u4) and Hadoop version 1.0.3 2.0.3 Setup Hive (for hivebench) Please make sure you have properly set up Hive in your cluster if you want to test hivebench. Or the benchmark willuse the default Hive-0.9 release which is included in package.
- We would like to show you a description here but the site won’t allow us.
- Hivebench provides an essential first step in this process. It is a digital laboratory notebook that helps researchers prepare, conduct and analyze experiments, methods, and protocols in one place, saving them valuable time. Hivebench has thousands of registered users who position it in the center of their research process.
This article has been updated in January 2018, in June 2018 with the addition of new ELNs and in August 2018 with complementary information. French version available here.
A new review has been written in 2019 with new information and new ELNs here.
Writing on paper is casual. Especially when you take notes on the lab bench.
So yes, taking notes on paper is easy. But let’s be honest: after the experiment, classify and recover data from a paper is time-consuming.
“I often feel like academic research is stuck in the 1990s,” says Dr. Thomas Crouzier, AlbaNova University Center, Connected Researcher's blog.
Data and procedures are often collected on paper when they can be computerized. And even if it sounds complicated at first sight, they are many advantages to using software to structure data.
Electronic laboratory notebook, also known as digital lab notebook or ELN, is a software made to collect and organize data and notes. So you can retrieve, and share your results easily. It can be so much more than a notebook made digital.
You might be encouraged to follow the 8% of scientists that already use electronic notebooks according to Klemen Zupančič, Business Development Executive of SciNote, during his interview with Labs Explorer.
If you are not convinced yet, Ingo Przesdzing presents the advantages of electronic laboratory books in this 30-minute video. In particular, he goes through the process of converting paper notebooks into ELNs.
Many companies develop electronic notebooks. Several options exist and you might be lost in the jungle of available products. So if you consider quitting the paper, you may be interested in the scoreboard developed by the ELN editor labfolder to evaluate your options. Also, find below the list of available electronic notebooks with their main features.
Labfolder
Online tool (SaaS), On-premise server solution • For all scientific fields • Free for up to 3 users • Made in Germany • On Labs Explorer •Visit the website
Labfolder is an electronic lab notebook with smart productivity features such as templates and advanced search. It also has a strong focus on usability, allowing anyone to start recording their experiments digitally without any training. Simon Bunger states that you can ask labfolder “Show me all the PCR primers for the WT1 gene, where the annealing temperatures are between 65°C and 72°C” to get the related information.
With its rigorous data security and integrity processes, Labfolder makes it easy for researchers to comply with FDA, ISO & GMP/GLP standards.
Labfolder can be tested for free without time limit and is available in English, French, and German.
Read more: labfolder's information on Labs Explorer or visit labfolder's website.
SciNote
Online tool (SaaS), software • For all scientific fields • Free (advanced paid features) • Made in Slovenia, the USA • On Labs Explorer
SciNote helps organize and access projects, experiments, and protocols. The interface is designed to be user-friendly, to safely store data and to access your data from one unique place. The idea is to avoid the user to transfer data from USB stick to computer and conversely.
SciNote aims to cleverly structure your documents and takes notes in a unique place. You can manage a whole project: from idea to publication. SciNote is an online tool shared among team members. Data are encrypted to ensure security.
SciNote is an open source platform. So modules can be created to fit project workflow. A library of modules is already existing and shared within the SciNote community.
LabCollector ELN
Online tool (SaaS) • For all scientific project management • Free (advanced paid features) • Made in France • On Labs Explorer
LabCollector is both an electronic notebook and a lab management tool. You can store your notes and track your samples.
Data stored are identified with a barcode to easily retrieve the right sample. LabCollector allows you to manage inventory. The system is customizable to adapt to the specificity of your lab, even for non-informaticians.
The notebook is accessible by the team with different access rights.
Labii ELN
Online tool (SaaS) • For biotechnology • Free (advanced paid features) • Made in the USA • On Labs Explorer
The Labii ELN helps to organize data documentation.
Labii ELN is a comprehensive ELN with LIMS to manage all your research data in one repository. It applied Natural Language Processing technology to extract useful data direct from your ELN.
It also enhanced data interpretation with customized bioinformatics pipelines. Several people can contribute or comment on a document.
About security, Labii ELN encrypted the stored data and keep a history of document versions. An electronic signature is available. Labii ELN also supports inventory management.
eLabJournal
Online tool (SaaS) • For life sciences • From €10 per user per month • Made in the Netherlands • On Labs Explorer
Besides the note-taking and data collection features, eLabJournal helps you manage the lab workflow. In particular, it allows tracking samples, managing protocols and SOPs, centralize supplies ordering and book instrument access.
All the files are shared within a team. The lab manager can assign tasks, and sign experiment if needed. Bonus: add-ons are available for integration with other tools, including Microsoft Excel.
LabRat-IF
Software • For life sciences, immunohistochemistry • Made in Sweden • On Labs Explorer
This software is made to design and manage protocols.
It actually generates protocols depending on the target molecule and chosen application. You can track and document your experiments thanks to QR-codes.
Different versions of the software are under designs for different experiments. LabRAT-IF is made for immunofluorescence applications.
Collaboration features are available in this version of the software.
Exemplar ELN
Online tool (SaaS) • For biology and chemistry • Price under request • Made in the USA • On Labs Explorer
Exemplar ELN is designed by Sapio Sciences. It provides an integrated solution to manage both ad hoc experimentation by scientists and lab process tracking. Exemplar enables the rapid building of complex process templates with zero coding, so scientists and lab managers do not have to wait for administrators to implement their requirements.
Exemplar also includes integrated analytics and data visualizations, all supported via a web browser on PCs and tablets. Exemplar has integrated biological and chemistry capabilities as well as registration of biological and chemical entities. Sapio Sciences offers its Exemplar solutions via the cloud for immediate signup and usage with no IT infrastructure required.
RSpace
Online tool (SaaS) • For all scientific field • Free • Made in the USA, the UK • On Labs Explorer
RSpace is developed by Research Space and helps organize data and resources. It allows storing sketches, chemical structure, annotation, and more. Protocols are organized as templates.
Documents can be created and shared among several team members.
The lab manager can assign tasks to people. RSpace connects with other tools like Dropbox, Google Drive, and even eCAT (see below).
Documents can be signed electronically.
CERF
Software • For all fields of commercial research • Made in the USA • From $300 per user license • On Labs Explorer
CERF is developed by Lab-Ally LLC. The ELN is a full-featured ELN to manage content, documents and knowledge assets. CERF allows PKI digital signatures and advanced semantic metadata. CERF features PKI digital signatures and advanced semantic metadata. CERF is best for commercial science organizations, pharma, and histopathology labs, or high compliance, regulated labs or businesses.
The ELN supports Mac, Windows and iPad systems. The client applications connect to a server that is installed on the customer’s hardware or on a cloud server. The system can also, if required, run on a secure LAN with no internet connection. Lab-Ally and their industry partners also provide professional consulting and validation services.
Hivebench
Online tool (SaaS), Software, Mobile app • For life sciences • Free • Made in the UK
Hivebench is a notebook designed for the biologist. It allows managing the protocol, inventory and data collections. The interface is intuitive and all features are available via both web and app versions.
A single lab manager can create groups of up to 10 colleagues. Electronic signatures and secure data trails can be tracked and reported on. Hivebench comes with an open source database of protocols as standard.
Benchling
Online tool (SaaS) • For molecular biology, biology, chemistry • Free (advanced paid features) • Made in the USA
Benchling allows to take notes, and track samples. You can store and manage data and protocol template. Several packages are available with several options designed for industry or academics needs.
Elements
Online tool (SaaS) • For chemistry • From $60 per user per month • Made in the USA
Elements help to design and conduct experiments. Its seems easy to retrieve data and document stored.
The collaborative features allow getting feedback and discuss with collaborators. Several packages are available with several options designed for university or industry needs. Chemicals can be drawn in your note easily with the ChemDraw® tool.
Hivebench Review
LabArchives
Online tool (SaaS), Mobile app • For all scientific fields • Free (advanced paid features) • Made in the USA
LabArchives aims to organize your notes and data. Capture of data from hardware or software can be automatized and integrated on LabArchives. The history of revisions is stored for you to retrieve older versions of notes. You can share and collaborate on documents with your colleagues.
Labguru
Online tool (SaaS) • For life science fields • Made in Israel, the USA
Labguru helps to design, conduct and document experiments. Each project can be linked to relevant resources like protocols, sample data or related publications.
The tool allows also inventory management.
Labguru is also made for CROs to monitor budget and order status.
eLabFTW
Software • For all research field • Free • Made in France
eLabFTW is an open source software. It is based on database management that the user sets up to organize its reagents, protocols, and so on. The time stamping of experiments protects the intellectual property of the user. eLabFTW supports teamwork with several members. Bonus: the software is available in several languages.
eLabFTW is a server software (PHP/MySQL) and should preferentially be installed at the institution level. Although it can be installed just for a team, or on a personal computer. It is supported by the Institut Curie and the French Institute for Research in Computer Science and Automation.
Mbook
Online tool (SaaS) • For chemistry • From €120 per license • Made in Spain
Mbook is interesting for chemist as it includes a molecular sketcher. Besides, the usual note-taking and data organizing features, you can analyze data directly on Mbook. Text and structure are searchable to retrieve information. You can track the workflow of experiment and projects. Several people can collaborate discuss on this tool.
Findings
Software, Mobile app • For all science fields • Free (with paid advanced features)
Findings help to organize the lab workflow. Findings support a shareable protocol library. You can design a protocol, take notes and get notified at each step of the experiment. Documents or results are attached to an experiment structure. The tool has a collaboration feature for lab managers to assign tasks. Findings stores your documents via Dropbox.
BIOVIA Notebook
Software • For chemistry
BIOVIA Notebook allows taking notes and documents with pictures, data, and chemical structures. Protocols are organized as templates. An electronic signature is available on this tool to ensure IP protection. Documents are shared with all lab members. BIOVIA Notebook provides integration with other cheminformatic software.
Docollab
Online tool (SaaS) • For all scientific project management • Free (advanced paid features)
Docollab is a collaborative workspace. It essentially produces and shares documents between several members of a team. All data are encrypted to ensure the security of data.
eCAT
Online tool (SaaS) • For all scientific project management • From €600 per user • Made in the UK
eCAT is a collaborative workspace. It essentially produces and shares documents between several members of a team. You can manage inventories and track sample using barcodes.
LabCloud
Software • For life science • Free • Made in the USA
LabCloud organizes your documents and data. The main feature of the software is to manage the inventory and instrument reservations. The software is connected with vendors to refill your inventory when needed. It provides integration with Microsoft Office®.
E-Notebook
Software • For biology, chemistry • Made in the USA
There are several versions of the E-Notebook from PerkinElmer depending on your research field. It allows to annotate, organize and visualize data in a single software. The software supports data entries from hardware and software.
ELN E-WorkBook
Hivebench Windows
Software • For biotechnology, pharmacology • Made in England
The ELN E-WorkBook by IDBS is a solution for global work management at a company level. You can manage and store files and data. You can design and execute protocols. The software supports data entries from lab instruments and other data management tools. The E-WorkBook provides information about the inventory.
LabWare ELN
Software • For life sciences, chemistry • Price under request • Made in the USA
LabWare ELN software goes along with the LIMS solution of the LabsWare company. The complete solution supports the lab management at a whole: experiments, workflow, equipment, customer and supplier orders, inventory, and more. The notebook interface is based on a spreadsheet structure with navigational tabs. Data can be captured directly from instruments or analysis systems.
NuGenesis ELN
Software • For life sciences, chemistry • Price under request • Made in the USA
NuGenesis is designed to document experiment, control protocols, ease collaborative work. It allows input from other software.
OpenLAB ELN
Software, Mobile app • For life science, chemistry • Price under request • Made in the USA
OpenLAB ELN is a software made to structure documents and easily takes note on the lab bench. In particular, you can dictate notes by voice. You can analyze data directly on the ELN: compare data sets, import metadata, and management protocols. It supports request tracking and collaborative features. An electronic signature is available on this software.
Projects
Software, Mobile app • For all science project management • From €24 • Made in the UK
This software helps you manage files. Project special feature is the timeline presentation of files to keep track of a project chronology. It keeps a version history of documents. Figshare is integrated into Projects, so the users can easily refer to data sets.
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We hope this list will help you decide which electronic laboratory notebook is relevant for your activities. This list may be not exhaustive, so do not hesitate to either share your experience or suggest ELNs.
The scientific community is well aware of the pitfalls and challenges associated with keeping and storing data. While there may be other data management tools, the most commonly used one is the unambiguous lab notebook. This innocent tool for keeping data is far from perfect—data can be lost, degraded, or otherwise compromised. Enter Hivebench, an electronic laboratory notebook (ELN) built by scientists for scientists. Hivebench is the answer for researchers who wish to manage data, track protocols, and collaborate.
Introducing Hivebench
Elsevier acquired Hivebench from Shazino, a research application developer based in Lyon, France. Hivebench was set to be integrated into the existing Research Data Management portfolio maintained by Elsevier. In a nutshell, Hivebench is an ELN that helps researchers conduct and analyze experiments, prepare experiments, and store methods and protocols in one place. This saves the researcher’s time. In addition, Hivebench is the only ELN available on the desktop (OSX), mobile devices (iOS), and the web. Aside from these, Hivebench is linked to Mendeley Data and other Elsevier tools. Thus, researchers can export their results to Mendeley Data. The acquisition of Hivebench is set to benefit funders and institutions as well. Hivebench is to be integrated with the “funder compliance check” module, which will solidify the link between data posting requirements and laboratory data.
Hivebench – Unlocking the full potential of research data from Bob Hendriks on YouTube
Features and Benefits
Hivebench has a plethora of features and benefits as compared to traditional, paper-based laboratory notebooks. It provides researchers and their colleagues a way to share protocols and data, which is hard to do when using paper notebooks. In addition, Hivebench allows users to access all the protocols and data at the same time, anytime. The progress of experiments can be stored in real-time. Considering how fragile, risky, and limited paper notebooks are, Hivebench presents a novel and concrete solution. Researchers need to spend a lot of time writing in a laboratory notebook, which doesn’t have search features and requires deciphering; however, Hivebench can allow seamless sharing of work. Comments and conversations can also be tracked real-time.
When using paper notebooks, researchers need to rewrite sections of drafts and deal with security issues with respect to their data. Aside from this, paper laboratory notebooks cannot comply with funders/FDA. There is also no uniform format for sharing. In contrast to this, Hivebench uses universal templates to share results in a consistent manner. It also complies with FDA/funder requirements. Researchers who use Hivebench can securely share their work with their colleagues. Moreover, automatic sign-outs are a feature of Hivebench. Data can be preserved in a non-proprietary format.
How Helpful Is Hivebench?
Paper-based laboratory notebooks are surrounded by peril: it is too easy to lose, destroy, and misinterpret them. There are instances when paper-based laboratory notebooks proved to be a recipe for disaster. Hivebench can clearly address these problems and a lot more. For example, losing your laboratory notebook in a fire is not unheard of. When fires do occur in laboratories, everything is lost. All the precious data and protocols are gone. Another situation is not having a lab notebook at all. Taking notes is imperative in research and not having a notebook is a common cause of frustration. In addition, it is difficult to search for data required by reviewers in a lab notebook, wherein you have to look through a lot of data.
Aside from these, losing data files is not uncommon. For instance, storing pictures of cells or analyzing DNA sequences is commonplace. However, what if the computer malfunctions? Everything is then lost. Hivebench stores all data on the same platform, which means that they will be accessible for years. Information stored in multiple locations is a problem, which removes uniformity in data storage and encoding. Hivebench can address this because it is the same wherever you access it.
Hivebench: write your lab notebook from Team Shazino on Vimeo.
Key Aspects and Drawbacks
Bee Hive Bench Plans
There are a number of key aspects that Hivebench is associated with:
Hivebench
- Improving sharing: Protocols are easier to access, common reagents and databases can be shared
- Increasing efficiency: Hivebench has an integrated notebook and calendar function that allows experiments to be scheduled so outcomes can be recorded
- Saving time: Protocols and previous results are easier to locate
- Reducing failure: It is easy to compare successful experiments with unsuccessful ones
- Signifying compliance with mandates: Funders are implementing mandates surrounding the sharing, storage, and capture of data.
There are, of course, some drawbacks to Hivebench:
Hivebench
- Protocol creation is rigid
- It doesn’t support the creation of tables
- Free Hivebench account is limited to 10 users
- Works only on iOS and OSX
There is no perfect system, however, Hivebench comes close. It’s still the best choice for researchers in terms of data collection and management.