Drawing Pictures in Electronic Notebooks for Data Review

• Journal List
• J Cheminform
• v.9; 2017
• PMC5443717

J Cheminform. 2017; 9: 31.

Electronic lab notebooks: can they replace paper?

Samantha Kanza

¹University of Southampton, Southampton, Uk

Cerys Willoughby

¹University of Southampton, Southampton, UK

Nicholas Gibbins

^aneUniversity of Southampton, Southampton, UK

Richard Whitby

¹Academy of Southampton, Southampton, Britain

Jeremy Graham Frey

^aneUniversity of Southampton, Southampton, U.k.

Jana Erjavec

ⁱⁱBioSistemika, Ljubljana, Slovenia

Klemen Zupančič

ⁱⁱBioSistemika, Ljubljana, Slovenia

Matjaž Hren

ⁱⁱBioSistemika, Ljubljana, Slovenia

Katarina Kovač

²BioSistemika, Ljubljana, Slovenia

Received 2017 April 7; Accustomed 2017 May 18.

Data Availability Statement

The datasets supporting the conclusions of this article will be available in the Pure repository for the Academy of Southampton, doi:10.5258/SOTON/405190. The datasets supporting the conclusions of this commodity are included within the commodity (and its Additional file 1).

Abstract

Despite the increasingly digital nature of society there are some areas of inquiry that remain firmly rooted in the by; in this instance the laboratory notebook, the last remaining paper component of an experiment. Endless electronic laboratory notebooks (ELNs) have been created in an attempt to digitise record keeping processes in the lab, but none of them have become a 'cardinal actor' in the ELN market, due to the many adoption barriers that take been identified in previous inquiry and further explored in the user studies presented here. The principal problems identified are the cost of the current bachelor ELNs, their ease of employ (or lack of it) and their accessibility issues across dissimilar devices and operating systems. Show suggests that whilst scientists willingly make apply of generic notebooking software, spreadsheets and other full general role and scientific tools to aid their piece of work, current ELNs are lacking in the required functionality to meet the needs of the researchers. In this paper we present our extensive enquiry and user study results to advise an ELN built upon a pre-existing cloud notebook platform that makes use of accessible pop scientific software and semantic spider web technologies to help overcome the identified barriers to adoption.

Electronic supplementary cloth

The online version of this article (doi:x.1186/s13321-017-0221-three) contains supplementary cloth, which is bachelor to authorized users.

Keywords: Electronic lab notebooks (ELNs), Notebooking software, Cloud, Semantic web, Scientific software

Background

In scientific research, communication is essential; between researchers, funding bodies, manufacture, and members of the public. Ideas need to be shared, bear witness disseminated, plans discussed, findings recorded, and errors corrected. Researchers may piece of work alone, only their enquiry is of little value to the scientific customs if information technology isn't disseminated. The scientific tape can act equally a legally binding tape that protects intellectual holding (IP) [39]. Historically the paper laboratory notebook and the scientific paper have been at the center of this scientific communication [12]; even so this is being slowly replaced by the arrival of digital technologies and the Cyberspace and the Web in particular [7].

Digital Technologies are shaping the way experiments are performed, results captured, and findings disseminated. Computers enable a myriad of functions that benefit researchers/scientists, they can be searched, shared, easily backed up, and readily accessed [xviii]. They facilitate interactive computation, electronic communication, multimedia, and digital information management [fifty]. Inside the lab, instruments are mostly computer controlled; computers are the main tools for capturing, analysing, and annotating data. Electronic laboratory notebooks (ELNs) are besides transforming the way that the scientific record is captured with a revolutionary transformation from paper notebooks to the digital capture of experiments [half dozen].

ELNs offer pregnant benefits to researchers by facilitating long-term storage, reproducibility, and enhanced availability of experiment records across multiple devices, ensuring standard operating process compliance and providing interfaces to instrumentation, supporting IP protection, collaboration, and open science [4, 21, 24, 43, 49]. ELNs eliminate the need for manual transcription and tin can be used past distributed groups [32], facilitate managing notes, and simplify the inclusion and curation of digital resources (east.thou. instrument data, analysis results) [ii]. While some systems are restricted to repositories of raw information and results, others have the potential to support researchers through the whole experiment lifecycle [17, 23].

More recently, semantic lab notebooks (SLNs) have utilised semantic web technologies to expose enquiry data as formalised metadata [10], and to link betwixt the different data sets collected throughout the experimental procedure [42]. Incorporating semantic spider web technologies within ELNs, using RDF and ontologies to enrich the data with meaning and context, provides new functionality such as making inferences near experiment types, and creates valuable links between experiment outcomes and their last reports [two, 5, 10, 23, 32]. Making ELN data machine readable increases interoperability, facilitates integration with third party tools and enables automatic generation of materials for deposition in an archive or publication [10], increasing the usefulness of the tools for researchers.

Although ELNs are existence increasingly used for industrial research, uptake in academia is limited [xix, 35]. This paper explores the current offerings of ELNs and Electronic Notebook software. Our enquiry conducted studies to investigate the attitudes of academics towards ELNs, and their desired functionality. It presents an overview of the barriers to adoption within academic environments, researcher behaviour, and key features for ELNs. Post-obit these findings, we discuss priorities for futurity ELN development and propose our Semantic Platform based ELN solution. Tablei introduces the user studies that will be discussed in this paper.

Tabular array 1

A table describing the different user studies that have been detailed in this paper

Study	Report dates	No of participants	Clarification
A—BioSistemika's Webinar Survey [3]	Oct 2015 and February 2016	228	Survey of electric current ELN usage
B—BioSistemika'due south ELN Survey	Mar–April 2015	196	Survey of ELN features, costs and barriers
C—University of Southampton's ELN study	Summertime 2016	103 ELNs	Written report of the current ELN market: active/inactive ELNs, ELN licensing and platforms
D—Academy of Southampton lab practice study (focus groups and lab observations)	Nov 2016–Mar 2017	33	Focus groups with physicists, chemists and biologists. Lab observations of four dissimilar chemical science labs at the University to better understand electric current lab practice
Eastward—Academy of Southampton's Dial-a-Molecule (DaM) Survey and iLabber Pilot Project	Sep 2011	Initial Survey—88 Commencement of Trial—92 Terminate of Trial—93	Surveys to gain knowledge and empathise attitudes towards using ELNs and issues identified with using the trialled ELN
F—Academy of Southampton'southward Communities Survey	2010–2015	94	Full details of this study tin be found in [48]

The market today

The electric current ELN Market is oversaturated with option; yet, despite the broad range of products available there is no obvious 'leader'. Additionally, the scientific community is withal resistant to using ELNs, despite the popularity of Electronic Notebooks. Electronic Notebooks that accept been subverted to ELN usage, current ELN offerings, and the attitudes to ELNs and their electric current usage take been examined and detailed in this section.

Electronic notebooks

Today's market has multiple offerings for Electronic Notebooks: (Microsoft Word, Office 365, Google Docs), Evernote [16] and OneNote [30], which take been evaluated for use as ELNs [33, 46, 47]. Oleksik et al.'s [33] report reported that the collaborative features of OneNote facilitated faster and easier sharing, and enabled simultaneous communication between researchers, irrespective of location. Users trialling Evernote as an ELN [47] said they appreciated the electronic affordances such as 'accessible from any online computer' and 'ability to search', just found that it was defective in domain knowledge; stating that it was 'simple and applied for some laboratories, but for others it does not offer features specialised for fields such as biology chemistry or quality assurance/quality control'. A residual may need to be struck between making an ELN usable across multiple disciplines, whilst nevertheless providing enough domain specific knowledge.

Whilst there are many attractive affordances of storing your notes electronically, it is of business organization to researchers whether their data is kept truly private or not, once it has been put into these services. Different service providers differ in their privacy policies. For example, Google Docs states that not only exercise the users maintain intellectual property of whatsoever content they create, content will non be shared with any third parties, and the user can take their data with them if they choose to go out Google Docs [20]. All the same, other services such equally Microsoft Office 365, may give contracted third parties access to their client data (which includes both personal data such as names and email addresses, just also information uploaded into their systems such as images and documents) to perform certain services [29]. An example of a privacy policy controversy is Evernote, where the default was for their employees to be able to read users content to ascertain the accuracy of their machine learning algorithms [44]. It is of import for researchers to be aware of privacy policies, and to ensure that research data is secure and can't be read past tertiary parties when using any software.

Electronic lab notebooks

Southampton University's ELN Market written report identified 103 ELNs [1, 27, 36, 42], 72 agile and xxx no longer agile; either due to discontinuation or purchasing by larger companies. The Active ELNs were further investigated to see which domains they supported, and their platform and licensing availability (Figs.1, ​ 2).

A chart illustrating the dissimilar domains represented past the active ELNs in the market place

A chart illustrating the licensing and platform data beyond the active ELNs in the market place

The different licensing categories and associated considerations are as follows:

• Paid for—This is a proprietary slice of software that tin be purchased, which may use proprietary information formats.

• Paid (with gratuitous version)—This is a proprietary piece of software that can be purchased, but which also has a version of this software which can be used for gratuitous; either as a trial for a stock-still period of time, or a version that has reduced functionality.

• Open up source—This is a product where the code behind the actual software has been made openly available then that anyone tin redistribute it and edit it as long as they conform to the licensing weather condition. Open Source products are often free, but non e'er, and could use either standard or proprietary data formats.

• Free—This is a product which is free to apply.

These findings illustrate an array of ELNs ranging from supporting specific disciplines (such equally eNovalys [15] which is aimed at chemists), to providing all-purpose solutions (such equally Kinematik's eNovator ELN [25] which aims to provide a multi purpose ELN that can be used in many different areas). All the same, a common cistron is that about of these ELNs require payment. Additionally slightly over 60% of them are web based/platform independent, with the balance only available on certain operating systems or without a disclosure of their platform compatibility.

At that place appears to be a proclivity towards ELNs that make use of pre-existing software. NuGenesis allows users to drag and drib Excel and Word files into their ELN, eLabJournal provides Excel inside it'south ELN, and LIMOSPHY uses Microsoft Word templates. This illustrates an increasing sensation that scientists do use notebooking software, even if they don't specifically apply ELNs. Additionally it suggests that there is a place for ELNs during the final write upward procedure, besides as during the physical experimental process. These ideas will be explored farther in "Proposal" department. In add-on to the market place investigations, electric current ELN usage was likewise researched. BioSistemika investigated ELN Usage, and the DaM survey looked at attitudes towards ELNs.

ELN usage and barriers to adoption

Despite the saturated ELN Market, results from the BioSistemika and DaM surveys indicated that whilst a big percentage of bookish users are considering or interested in using ELNs (as shown in Fig.3; Tableii), they are lacking in uptake in academia [xix, 35]. Many scientists extensively use computers, yet continue to utilise newspaper notebooks throughout their experiments; highlighting that computer illiteracy or an aversion to technology cannot fully explain resistance to ELNs [26, 28, 41].

The results of the BioSistemika Webinars: Are you lot using electronic laboratory notebooks (ELNs) in your Daily Lab Routine?

Tabular array 2

Attitudes towards ELNs from the respondents of the Dial-a-Molecule'south 'Potential employ of ELNs in Academia' Survey

ELN sttitudes	%
Awareness of ELNs	98
Using an ELN in their enquiry group	11
Stiff interest in implementing one or finding out more most them	76

The Academy of Southampton'south Lab Practice Report asked users about their ELN usage and experiences. Some participants had used ELNs such as LocalWiki, LabTrove, Blog3, BioBook, Enovalys and an industrial one on a brusque term basis. The industrial ELN was unfavourably described, whilst the other ELNS were merely deemed useful for sure purposes. I participant constitute Enovalys very useful for inorganic work, simply lacking the required functionality for their transport runs. Equally, participants who tried LabTrove and Blog3 constitute some of the elements useful in certain situations, merely all defaulted back to Word documents. Ane participant suggested that this was the case considering it did not contribute in a systematic style to their work.

There are therefore challenges and barriers to adoption of ELNs. Figure4 and Tabular arrayiii illustrate the key barriers that our studies identified, and these are described in more than depth in the following sections.

The barriers of using an ELN from both a research lab and a diagnostic lab

Table 3

Categorised barriers of ELN adoption from the Dial a Molecule iLabber Pilot Projection: Potential Uses of ELNs in Academia Survey

Category	Barriers	Percent of 169 (%)
Cost	Up front costs and licensing fees	74
	Additional infrastructure costs (e.k. computers)	27
	Futurity development and costs of applications	90
	On-going costs of the organisation	93
ELN attitude	Only makes sense if the whole section adopts it	20
	Belief that students/postal service docs would resist adoption	11
Ease of Utilise	ELN was likewise difficult to use	22
	Does not capture the right information for me	7
	Difficult to capture some kinds of information in an ELN	80
ELN access	You'd demand to enter information in both the lab and write-up area	74
	No easy admission to appropriate hardware in the lab	12.5
Information compatibility	Data will exist tied into a commercial bundle	84
Other	Other	11

Cost

As shown in Table3, a large per centum of survey respondents indicated that cost was a significant barrier to ELN adoption [four, 19, 35]. This includes financial outlay, staff hours, troubleshooting, and the fact that long-term apply is likely to require on-going maintenance and support. At that place are besides concerns about the required database administration and back up, with suggestions that having professional IT staff to help with setup and maintenance would exist pivotal.

One respondent experienced sharp cost-increases in database maintenance and upgrade costs after an initial discount. Other concerns are service providers not competing to keep costs downward, and the potential toll of storage space; indicating disincentives if the Academy charges groups for storage space. Effigy4 illustrates a willingness to pay up to $50 a month for an ELN, merely non $100; suggesting that ELNs reach a bespeak where they are considered 'also expensive' (Fig.5).

The maximum costs that the respondents of the BioSistemika's ELN survey would be willing to pay for an ELN per month, from the perspective of those in Research, and with Purchasing Power

Other comments queried whether funding was available for ELNs in universities; suggesting that web-based systems could significantly cut costs, as they require less hardware.

Every bit evidenced past Fig.2, most of the ELNs bachelor in the market place are proprietary pieces of software that crave purchasing, in that location are also some free and open source offerings bachelor. The free options would clearly accept the reward of being cheaper to run and test merely may accept disadvantages depending on the nature of the software. The paid for and free software model (one of the categories in Fig.2) will have enterprise users to generate its revenue, and are able to offer reduced gratuitous versions to other users to generate recognition; providing the benefits and stability of proprietary software with a potential lack of price. However, the fear is that other standalone costless offerings are more than likely to disappear, potentially alongside the enquiry information. Some of the inactive free ELNs that were identified every bit role of the University of Southampton's ELN Written report were listed on [ane, 24] with websites that had seemingly vanished with no new obvious location. Open Source software is often gratuitous (although non always) and has a pregnant advantage over proprietary software with respect to their potential longevity. Both Open Source and Proprietary projects will always be at adventure of ceasing to keep, either due to lack of funds or the original developers leaving the projection. However, given the licensing of Open Source projects which makes it possible to view and change the source code, other developers are able to access, update and support the software.

Ease of utilize

Another challenge is the perceived 'ease of use' of paper notebooks compared to electronic systems. Paper notebooks are considered easier to utilise, input information to, read, transport, inexpensive, readily available, 'turn on' instantly, have infinite battery life, are socially acceptable during meetings, and require no grooming and minimal IT support [4, 8, 11, 19, 28, 50]. Whereas, ELN software for taking notes is considered more hard to use, timely and less flexible; leading to anxieties about ELNs stability, accessibility and availability [14].

Our interactions with researchers and ELN users demonstrate that ease of utilize is vital to adoption. In the DaM survey, 99% of respondents indicated that ease of employ would influence their ELN pick, with almost 80% rating information technology every bit very of import. One comment reflected the desire for a flexible generic solution, rather than an ELN designed for a specific research area, due to anxieties that their research "doesn't fit neatly into 1 category".

Attitudes to ELNs

Adopting an ELN only makes sense if the whole department adopts it, which allows for sharing costs and training; repositories, consistency and use of standards could also be relevant [10, 42]. Several comments reflected their assumption of students and postgrads rejecting ELNs through "resistance to change in some groups", noting that some students didn't like their experiences of ELNs, and might consider using them as an "additional burden".

Access to ELNs

In the Uses of ELNs in Academia survey, 74% expressed concerns about needing to enter data in both the lab and write-up expanse, due to a lack of suitable hardware or software capabilities to facilitate ELN usage inside and exterior the lab. This can lead to copying and pasting printouts into paper notebooks and manually transcribing data between notebooks and computers; which tin can issue in data loss, transcription errors and records stored haphazardly [9, 32]. Popular suggestions were to use mobile computers or tablets for portability in and out of the lab, and that web-based ELNs could improve accessibility.

Lack of appropriate hardware access in the lab lead to 12.v% of participants in the Mail Airplane pilot Survey ceasing to use the trialled ELN, and resulted in several needing to perform tasks manually. Other anxieties frequently raised, included risk of damage or contamination, security, 'hassle' of carrying laptops effectually, shortage of computers for sharing, lack of demote space for computers, ELN not supported on chosen mobile platform, and lack of wifi access. Primary workarounds for these issues appeared to be printing out experiments, writing up experiments retrospectively, or using newspaper notebooks aslope the ELN.

Software and system integration and compatibility

Researchers use different operating systems, but both the ELN Market written report and comments from the DaM survey revealed a lack of availability of ELNs for Macs. It was suggested that iPads could work every bit a shared notebook due to their ease of transport, although software would need to be compliant with iOS and other mobile platforms, or web based. A perceived bulwark was linked to integrating ELNs with existing infrastructures. The DaM Surveys had similar concerns that users might be expected to purchase new ELN software at each operating system upgrade; which could contribute to system costs, support costs, and additional training requirements.

Electronic pen data entry, integration with digital repositories for archiving purposes and bibliographic management have as well been mentioned with regards to integration with existing tools. The DaM Pilot Program elicited a demand for software compatibility, database integration, electronic data, and other 'common software' (e.g. Word and Excel), and options to purchase add-ons for increased functionality. Users found problems using the ELN on a 64-bit operating organization and on macs, or with Chemdraw, office attachments, uploading photographs, and "…information technology was too cumbersome to import files from our current systems…". ELN information input seems to have been a recurring issue, alongside failings in basic expectations about data management that heightened existing anxieties.

Data compatibility and portability

In the DaM Airplane pilot survey just under 70% expressed business organization about the ELN capturing data easily, with 81% considering automated experiment data capture important. Comments indicated that capturing a range of data is important, but raised concerns almost the difficulties of instrument integration, partly due to a lack of standards between unlike manufacturers. Many comments expressed frustrations about not beingness able to link to specific experimental data such as spectroscopic results.

Several comments indicated worries near the ability to extract and move data between different ELNS and machines; these concerns chronicle to price hikes with a provider, longevity of commercial packages, and irresolute establishment. Other comments addressed issues of proprietary formats including previous bad experiences of "existence tied into data formats" or beingness left with only a PDF of their data; although the desired transferral formats differed between respondents. Some comments embraced the importance of open data and not existence tied to a particular commercial parcel, suggesting an open up source ELN to resolve the trouble. This suggests that researchers perceive open source offerings to be more likely to use standard information formats rather than proprietary formats. Concerns were as well expressed regarding accessing databases and notebooks beyond different machines, suggesting that users expect their information to be stored locally or in a centralised system, and are concerned about information security.

What practice users practise?

What users say they exercise doesn't always lucifer their actions; therefore subsequently establishing the main adoption barriers, we investigated how the researchers really worked. Iv focus groups were run with 24 postgraduate chemists, physicists and biologists to hash out their electric current practices. Additionally, four different chemistry labs were observed to see how scientists operated there.

Results

We found that dissimilar researchers vary their working patterns and note-taking, and have contrasting needs when it comes to sharing records with others. Therefore a 'ane size fits all' approach to tool design wouldn't be effective. Tools demand to provide considerable flexibility and customisation to accommodate different needs. The loftier level results of these activities across the different disciplines are presented in Table4, and will exist farther discussed afterward on in this section.

Tabular array 4

How the physicists, chemists and biologists who took part in the University of Southampton Focus Groups perform unlike work tasks with respect to whether they employ newspaper or electronic systems

Category	Tasks	Biologists	Chemists	Physicists
Recording notes	Experiment notes	Paper—Lab Book	Paper—Lab Book Electronic—Data	Paper—Lab Book Electronic—Data
	Thinking nearly piece of work notes	Paper—Lab Book	Paper—Lab Book Electronic—Google Tasks	Newspaper—Lab Book Electronic—Google Keep
	Literature notes	Paper—Print papers/handwritten notes Electronic—reference managing director	Paper—Impress papers/handwritten notes Electronic—reference managing director	Newspaper—Print papers/handwritten notes Electronic—reference managing director
Organising notes		Paper—Lab Book by engagement/contents page	Paper—Lab Book past appointment/contents page Electronic—By codes (linking to Lab Volume) and by sample/experiment	Paper—Lab Book past date/contents page Electronic—by codes (linking to Lab Book) and by category/experiment
Searching		Paper—flip dorsum and search by date	Paper—flip back and search by appointment Electronic—sort past date/code, or keyword search	Paper—flip dorsum and search by engagement Electronic—sort past date
Linking data		Paper and Electronic notes linked by appointment	Paper and Electronic notes linked by codes	Newspaper and Electronic notes linked past date
Writing reports		Electronic—Word/Powerpoint	Electronic—Discussion/LaTeX	Electronic—word/LaTeX
Performing calculations and scientific functionality		Paper—solve Electronic—check (Excel/GraphPad)	Newspaper—solve Electronic—Bank check (Wolfram Alpha)	Newspaper—solve Electronic—Check (Excel/XMGrace/Spartan/PyPlots/R/CSV)
Use of Technology in the Lab (accessibility)		Electronic—Telephone pictures/recordings	Electronic—Phone/camera pictures, Emails, Blogs, USB	Electronic—Phone pictures/calendar, Emails
Archiving and backup		Newspaper—Mostly no backup (some photocopies) Electronic—Uni computers/shared drives/the cloud/hard drives	Paper—Mostly no backup (some utilize carbon pages) Electronic—Uni computers/shared drives/the cloud/hard drive	Paper—No backup Electronic—Uni computers/shared drives/the cloud/hard drives
Intellectual property		Electronic—Secure data kept on hard bulldoze in locked draw	Electronic—No cloud software for industry sponsored students	Electronic—No cloud software for manufacture sponsored students
Collaboration		Newspaper—Lab Volume	Paper—Lab Volume Electronic—shared drive/grouping folders	Newspaper—Lab Book Electronic—shared drive/group folders

Give-and-take

The biologists and physicists from these focus groups were more often than not uniform in their methods, whereas the chemists were more diverse, highlighting differences in their approach even inside a single discipline.

Computational chemists used some software, with sporadic use of lab books and scraps of newspaper, whereas the 'wet' chemists had stringently organised lab books for dissimilar tasks. I chemist used blogs and Discussion documents aslope their paper notebooks, and the crystallographers relied heavily on their paper sample books. The inorganic and organic chemists used paper lab notebooks during experiments, and merely used lab computers to admission the instruments they were linked to. Annotation-taking differed depending on the state of affairs. For experiments, the lab volume was typically used to record observations and initial values. The chemists recorded dissimilar types of data including energy values, simulations, temperature, masses, observations, schemas, and protocols. These findings accept similarities to Reimer and Douglas's [34] work, illustrating how information recorded remained much the same; but likewise demonstrating that different chemists possess contrasting needs for recording their notes. Constructing one's own 'templates' or other mechanisms for standardising information capture appears to be common in bookish environments [forty]; therefore providing capabilities to facilitate this is likely to be pop [ii, xl]. Allowing users to edit their own templates poses challenges. This is illustrated by a comment from i of the lab ascertainment participants, who resented being asked to utilise a template rather than expressing themselves in their own style.

Chemists also differed in how they linked their paper and electronic notes. The physicists and biologists linked them by date, whereas the chemists inconsistently used a variety of codes; reflecting the personal nature of note organization [40]. Despite their differing lab work, there was a common theme of using instruments (e.grand. X-ray machines or diffractometers) to read data, and linking statements in their lab book to reference electronic data location and any data values that required inputting to other software. In some situations information technology may be necessary to capture some information on paper, and ELNs therefore need to facilitate the inclusion of such information with the research record.

Different disciplines had varying restrictions on what equipment could exist taken into the lab. The biologists didn't have specific restrictions, although 1 biochemist mentioned that there were concerns about bringing in outside equipment in case of contagion. The physicists couldn't bring equipment into their cleanroom to avoid contaminating the surroundings; contrastingly, the chemists wouldn't accept technology into the lab in order to avert dissentious it with chemicals. Computers in the lab weren't oft online, and well-nigh were continued to specific instruments. When asked, participants indicated a reluctance to use instrument dedicated computers for any other purpose, such as making notes, accessing documents remotely, or using cloud software as they didn't have network access. One chemist stated that "once you've started doing something one way, you don't desire to alter it".

Scenarios

To investigate the participant'southward current searching and fill-in procedures, they were presented with three scenarios to discuss (illustrated in Fig.six):

• Imagine yous're trying to locate some work from 6 months agone, how would you locate you notes and associated data?

• Imagine there's a burn in your lab and all of your paper notebooks are destroyed, how much piece of work would yous lose and how could you go about recovering information technology?

• If you vicious under a bus tomorrow, and were temporarily indisposed, how would your supervisor/industry sponsors/colleagues access your piece of work?

For Scenario 1, participants revealed that they organised their lab books chronologically, and the most common method of locating previous piece of work was to go back through their lab book by date to locate work from a particular time period. Similarly to locate previous work on a computer participants said that they would search by engagement to find the advisable data files, or would search by proper name if that proved unsuccessful.

Cartoon depicting three different scenarios, Scenario one: Trying to search for some work/data half-dozen months afterwards, Scenario two: What would happen if your lab was set on fire and you lost everything in at that place, Scenario 3: If yous were indisposed for a while how would your supervisor/enquiry group access your piece of work

Scenario 2 provoked different reactions. Some participants were unconcerned at the prospect of losing their lab books, and thought reproducing what was needed wouldn't take as well long, every bit a lot of the information was simply 'useful in the moment', or a list of things that didn't piece of work. Whereas other participants elicited responsed such as 'I'd be ruined', 'a nightmare', 'might as well cease my Ph.D. at present'. Particularly with reference to the idea of their labs catching fire, several participants seemed more concerned at the idea of losing their lab samples or compounds; suggesting that perhaps their lab books would not be the biggest loss in a fire.

Scenario iii revealed that generally participants don't have measures in identify to enable their supervisors to admission their work if something happened to them. One of the biologists had a specially strict supervisor who required their students to photocopy all of their lab books and work, but that was a rare exception. It did still transpire that the participants believed that other group members would probably be able to access their work and give information technology to their supervisors, but didn't believe that they would be able to follow their lab books or the structures they'd put in place to link together their paper and electronic notes.

This continues the earlier theme about participants showing less concern towards bankroll up their newspaper based work. They are apparently enlightened that these scenarios could occur, but clearly don't perceive them as probable or serious enough to merit much pre-emptive grooming, apart from circumstances where their supervisors have put procedures in place. Capturing notes and data electronically has articulate backup and archiving benefits. Not only tin electronic data be automatically backed up and deeply stored, but the information tin can become accessible beyond multiple locations. Outdated data tin can be archived then that it tin exist retrieved later if needed, or to be shared with other researchers through degradation or publication.

What practice users want?

Having discussed with the users what they actually practise, this department will await at what features the users say they desire, with data taken from all studies B, D, East and F.

These accept been grouped according to the different categories in "What do users practise" section in add-on to a new category of project activities that came out of this research. These features have besides been linked to the associated priorities of the iLabber pilot project for those who constitute these features very or quite important; and it's been noted which barriers these features aim to accost.

The full breakup of priorities from the iLabber Airplane pilot Project are shown in Fig.7.

The main priorities of different ELN features from the respondents of the iLabber Piilot Project, ranging from whether respondents saw them equally not important to very important

Proposal

Based on the needs elicited from our user studies, we formulated a proposal of how to construct an ELN surround that would fit with these requirements. The majority of ELNs have been created from scratch including the underlying 'notebook' part [31, 32, 42]; an alternative would be to build on acme of a generic Electronic Notebook (which are more popular than ELNs) with domain specific features. Many of these Electronic Notebooks already have collaborative cloud based features, and could be further expanded with domain noesis and Semantic Spider web technologies. Additionally, based on our marketplace research, despite the amount of available ELNs there are a minority that are available as free/open source platform independent entities that scientists tin can use on any device, suggesting a gap that could exist filled with this blazon of ELN.

Visions

Every bit part of this vision BioSistemika used their ELN survey to create their own ELN, sciNote [38]. Taking the path towards interoperability, sciNote has been designed in a modular way and released under the Open up Source licence (Mozilla Public Licence). Based on the user needs they are developing new add-ons and at the same time they are encouraging the customs to develop their own add together-ons, similar to the packages concept of R-statistical. In this fashion every lab will be able to design their own ELN to fit their needs, which will assist them manage their projection, share inquiry, gather the metadata directly from instruments and connect with existing software and databases.

Southampton Academy has looked at the features the users want (shown in Tabular array5) and formulated how these could be achieved using an Electronic Notebook Platform as a base. In that location is a large overlap of features between Electronic Notebooks, ELNs and SLNs and the master features required by an ELN already be in generic Electronic Notebooking software [34]. Furthermore, using a cloud based Electronic Notebook platform would gainsay some of the accessibility problems and facilitate the collaboration requirements of the users, and incorporating Semantic Web technologies would provide an improved (semantic) search (the acme priority listed in Fig.seven) and allow for metadata/tagging (as requested).

Table 5

These are the desired features elicited from the dissimilar user studies, linked to the priorities and barriers they relate to from the Dial-a-Molecule surveys

Category	Desired Features	Priorities (DaM)/Addressing Barriers
Recording notes	Simple to install Personalisable Postal service-it notes TODO lists Create default values Like shooting fish in a barrel to write in as a paper notebook Facilitate dissimilar experiments Range of experiment templates	55.6%—Saving time over the paper notebook process is of import Bulwark: Ease of employ (3.ii)
Organising notes	Indexable/highlightable Contents tabular array/overview screen/timeline Spellchecker Tag/classify notes and experiments Store metadata Utilize of standard vocabularies (ontologies/measurement techniques)	eighty.two%—Improved quality of record keeping is important
Searching	Keyword/filtered search Data traceability Avant-garde searches by chemical structure Include reactions schemes in search results Vocalization searches Sortable results	90.half dozen%—Improved ability to search and re-apply documented information is important
Linking data	Upload/link files, images and data files to notes Link between unlike notebooks Link to reference managers Dropbox-esque features (automated data update) Automatically link to external chemistry resources	73.six%—Improve access to information as linked data through ELN is important Barriers: Information Compatibility and Portability (3.6)
Writing reports	'Generate Study' push to generate a publication ready report Integrate and store dissimilar types of documents (Excel, Discussion, PDF, Pictures, Handwritten notes) Copy sketches into notebook Paper notebooks integration Digital pen integration Migration tools Export functionality	Barrier: software and system integration and compatibility (3.5)
Performing calculations and scientific functionality	Perform calculations, formulas and equations as easily as paper Create sketches and diagrams Recognise a chemical when entered Gamble Cess Templates/view electronically Flags for unsafe chemicals Index of COSHH materials Global database of chemical values Notifications for approvals Sign off entries to brand them non editable	sixty.4%—Easy inclusion of condom data is important
Utilise of Technology in the Lab (accessibility)	Web Based/Platform Independent Tablet/Smartphone Compliant Text recognition, cartoon and photo capabilities Usable in the lab like a paper notebook Vocalization capture Built in language for extensibility	79.iii%—Access to notebook from more locations is important Barrier: Access (3.iv)
Archiving and backup	Secure storage, backup and archives Downloads/printing	87.viii%—Secure automatic backup of data is of import
Intellectual belongings	Secure access Different access levels for users	37.8%—Better protection of IP is important
Collaboration	Shared files/notebooks Standard list of instruments and reagents Link related people and notebooks Coordination for Open up Source and Access Sign upwards and 'get involved' pages Configurable stand-alone to deed as portals for projects and landing pages for collaborators Enable users to find out who is working on like molecules of reactions (requires inbuilt agreement of molecules)	63.2%—Improve ability to collaborate and share information is important
Project activities	Contempo activity feed with notifications Page statistics Bulletin boards Moderate comments	64.1%—Improved group/project direction is important

A cloud based ELN

At that place will always exist concerns about IP with regards to using Cloud based services. The Academy of Southampton's Lab Exercise study elicited that users with industry sponsors were less likely to use Cloud software. Information technology is thought that once data is 'in the cloud' users are no longer in control [thirteen], and that like with any electronic service at that place is the potential for data breaches [45] even so many precautions are taken. However this business certainly isn't restricted to electronic data. Some of the biologists from the University of Southampton'southward Lab Practice Report said that they didn't consider their work to be safe at conferences every bit people may have photographs of their posters and steal their ideas, and some of the chemists were aware that previous members of their research group had been 'scooped' which resulted in tightened security measures across the grouping. Despite this, deject computing is advantageous in that it can provide big volumes of storage and computing power that are accessible from any location [13, 45], and information technology'due south worth noting that just xviii.9% of respondents in the iLabber Pilot Project Survey thought that 'Better protection of IP' was 'Very of import', ranking significantly below Improved search and secure automatic backup of information, both of which lend themselves greatly to our proposed methods.

Proposed features/blueprint

When investigating the features our users desire, we realised that approximately 40% of these features are already implemented within cloud based electronic notebooking software, and the rest of the features are either domain specific or could be achieved using semantic spider web technologies. Figureeight shows these desired features elicited from our user studies detailed in Tabular array5, which are supported past previous ELN research work [4, 18, 22, 34, 37, 42, 46].

The desired features that have been elicited from the unlike user studies. Categorised past whether they are features already included in a deject based notebook, and then whether they fall into the category of an ELN domain specific feature or a semantic feature

We believe that this arroyo and the subsequent ELN environment that volition be developed can mitigate the current barriers and concerns, these are detailed in Table6.

Table 6

How the proposed system could mitigate the barriers elicited from the Dial a Molecule iLabber Pilot Projection: potential uses of ELNs in Academia Survey

Bulwark	Mitigation
Price (3.ane)	ELN would exist free
Ease of use (3.2)	Using a pre-existing Electronic Notebook would mean users are already be familiar with the system and rather than building the notebooking side from scratch information technology would use a tried and tested product
Attitudes to ELNs (3.3)	Adding a domain/semantic layer to software scientists already use might improve attitudes towards this type of ELN
Access to ELNs (3.four)	A deject based ELN tin can exist accessed anywhere with an internet connection on any desktop or mobile device (including phones and tablets)
Software and arrangement integration and compatibility (3.5)	Cloud software is platform independent
Data compatibility and portability (3.6)	Using cloud software to shop data means it tin can exist accessed beyond multiple devices. The cloud notebook would permit the user to consign their inquiry data in a variety of common information formats.

Therefore we propose that edifice a semantic ELN on height of an existing cloud infrastructure or platform would allow us to make use of these pre-existing features, provide a solid notebook base aligned with software scientists already employ, and would also help gainsay the current adoption barriers. The ability to adapt documents and control input provided past a platform such as Google Docs enables much of the functionality needed for an ELN (eastward.g. in Fig.9).

An example of adding domain specific features to a pre-existing cloud notebook tool

Conclusions and future work

Our user studies accept made 1 thing very clear, we cannot currently hope to fully replace the paper lab notebook. Until we take the technology where a screen can be written on every bit accurately and easily equally paper; and labs have cheap, durable and hands replaceable tech to employ instead of newspaper, information technology volition always prevail for some tasks. We likewise need to stop thinking of ELNs equally direct replacements for paper lab notebooks that are only useful during experiments in the lab, and consider them in the wider context of the whole experiment process. Therefore we need to build a system that works with paper, and codify a new digital practice for scientists to use in their electric current lab environs.

Despite some scientists preferring paper notebooks, they still frequently apply technology in their work. Many store information electronically, and use note-taking software such as Word and Evernote to write up their notes, Excel to handle their figures and graphs, and some use speciality software for specific tasks. The deject is also widely used to fill-in work and make it available across different locations. Therefore nosotros need to first considering ELNs that can work in this context, and to work out how nosotros can re-use existing successful software to create a better ELN platform.

We propose that we need an ELN environment that tin can serve as an interface between paper lab notebooks and the electronic documents that scientists create; that is interoperable and utilises Semantic spider web and cloud technologies. It would fulfil all of the software needs described in "What do users want" department and provide a centralised location for the scientists to shop their notes. Whilst the ideal long term goal is that adoption of an ELN alongside extensive laboratory automation removes any demand for paper, realistically electric current engineering is such that information technology is desirable that ELN solutions work alongside paper for the foreseeable time to come. We believe that ELNS will significantly improve reproducibility of scientific experiments, contribute to the data traceability and data annotation and enable scientists to collaborate and share results in an intuitive fashion. The wider adoption of ELNs will facilitate interoperability which will ultimately change the means scientists perform experiments and manage their data. There'due south a not bad potential for future work in these areas, as an ELN that follows our vision has withal to be created, and equally hardware and applied science as a whole advances, nosotros will be able to support even more of the experimental process digitally.

Authors' contributions

SK carried out Study C and Study D. CW carried out Written report F and was involved with Written report Eastward alongside RW who designed and originated the survey. JE, KK and MH carried out Studies A and B. KZ/BioSistemika designed the surveys, did survey analysis and developed a concept of sciNote ELN together with MH. SK, CW and JE all contributed to writing the manuscript. NG and JGF helped typhoon and revise the manuscript, participated in the blueprint of the research, and the analysis of the results. All authors read and approved the concluding manuscript.

Author informations

SK is a final yr iPh.D. Pupil in Web Scientific discipline at the University of Southampton. Her primary research focus is Semantic Spider web technologies, and she is looking at bringing the modernistic ability of the web to chemical enquiry. She has a First Form M.Eng. Degree in Computer Science and worked as a software developer before starting her Ph.D. CW has recently completed a Ph.D. with Southampton University investigating annotation-taking behavior of scientists in the lab and the design of tools to assistance them capture and brand use of their experiment data. Before undertaking research at Southampton, she worked at IBM U.k. Laboratories as a software engineer specializing in software usability and information architecture. NG is an associate Professor in Informatics at the University of Southampton. His chief enquiry interests are in the Semantic Web, hypertext, and distributed information systems. RW is a Professor of Organic Chemistry at the University of Southampton. He originated and leads the 'Punch-a-Molecule' Yard Challenge (www.dial-a-molecule.org), which has the 20–40 years aim of making the synthesis of new molecules every bit quick and like shooting fish in a barrel every bit it currently is to order a commercial compound. He is interested in total synthesis, menstruation chemistry, molecular electronics, and cheminformatics. JGF is a Professor of Physical Chemical science at the University of Southampton. His interests bridge experimental light amplification by stimulated emission of radiation spectroscopy and imaging, though chemic informatics and modelling, to the wider area e-science and digital economy. JE has a Ph.D. in Microbiology and Biotechnology. She always follows the latest trends in the Life sciences and believes that smashing software will exist a crucial tool for wet lab or dry lab scientists in the almost future. KZ has a Ph.D. in Genetics. He has created several successful companies and he strongly believes that platforms that are able to connect with your instruments and other software seamlessly volition assist in creating digital laboratories of the future. MH has a Ph.D. in Gene expression technologies. Based on his ain experience, he has dedicated his career to developing new software products for researchers. KK has a Ph.D. in Virology. She has a special involvement in laboratory management improvement and automation which would enable researchers dedicate more time to their research and innovation and get out tedious routine laboratory tasks to smart software and instruments.

Acknowledgements

We would like to thank all of the people who took office in the unlike user studies.

Competing interests

BioSistemika's ELN Webinar Survey and ELN Survey were done equally a office of the ELN market research before they started with the development of sciNote Open Source electronic lab notebook. The results of BioSistemika's market place research complement nicely with the information gathered by the University of Southampton. They highlight the current land of the ELN market and show in which direction existing and new ELN solutions should become in order to meet the expectations of the users. JGF is involved with the LabTrove ELN projection (www.labtrove.org).

Ethical approving and consent to participate

Specific ethical approval was obtained for Study 4 (the almost recently conducted study). This study was approved by the Academy of Southampton's Ethics Committee for the Kinesthesia of Physical Sciences and Engineering. Focus groups—ethics application ERGO/FPSE/18246. Participant observations—ideals application ERGO/FPSE/18448.

Availability of data and materials

The datasets supporting the conclusions of this commodity will be available in the Pure repository for the University of Southampton, doi:10.5258/SOTON/405190. The datasets supporting the conclusions of this article are included within the article (and its Additional file 1).

Funding

This piece of work was supported by the Web Science Eye for Doctoral Training at the Academy of Southampton, funded past the United kingdom Engineering science and Concrete Sciences Research Council (EPSRC) under Grant No. EP/G036926/i. This piece of work was also supported by the following groups Digital Economy IT as a Utility Network + under Grant No. EP/K003569/1, the South East Regional e-Research Consortium under Grant No. EP/F05811X/i, and PLATFORM: Terminate-to-End pipeline for chemical information: from the laboratory to literature and back again, nether Grant No. EP/C008863/i. The Dial-a-Molecule work was also supported by the following Grants: EP/H034447/1 and EP/K004840/1. BioSistemika'due south ELN Survey and Webinar were financed by BioSistemika LLC as a part of their ELN market research.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Abbreviations

DaM	Dial-a-Molecule
ELN	electronic lab notebook
ELNs	electronic lab notebooks
IP	intellectual property
RDF	resource description framework
SLNs	semantic lab notebooks

Footnotes

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-017-0221-3) contains supplementary material, which is available to authorized users.

Correspondent Information

Samantha Kanza, Email: ku.ca.notos@80g11ks.

Cerys Willoughby, E-mail: ku.ca.notos@ybhguolliw.syrec.

Nicholas Gibbins, E-mail: ku.ca.notos.sce@gmn.

Richard Whitby, Email: ku.ca.notos@ybtihw.j.r.

Jeremy Graham Frey, Email: ku.ca.notos@yerf.thousand.j.

Jana Erjavec, E-mail: moc.akimetsisoib@cevajrej.

Klemen Zupančič, Email: moc.akimetsisoib@cicnapuzk.

Matjaž Hren, Email: moc.akimetsisoib@nerhm.

Katarina Kovač, Email: moc.akimetsisoib@cavokk.

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