Journal:Electronic laboratory notebooks in a public–private partnership - Revision history

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	\|title_full = Electronic laboratory notebooks in a public–private partnership		\|title_full = Electronic laboratory notebooks in a public–private partnership
	\|journal = ''PeerJ Computer Science''		\|journal = ''PeerJ Computer Science''
	\|authors = Vaas, Lea A.I.; Witt, Gesa; Windshügel, Björn; Bosin, Andrea; Serra, Giovanni; Bruengger, Adrian; Winterhalter, Mathias; Gribbon, Philip; Levy-Petelinkar, Cindy J.; Kohler, Manfred		\|authors = Vaas, Lea A.I.; Witt, Gesa; Windshügel, Björn; Bosin, Andrea; Serra, Giovanni; Bruengger, Adrian;<br />Winterhalter, Mathias; Gribbon, Philip; Levy-Petelinkar, Cindy J.; Kohler, Manfred
	\|affiliations = Fraunhofer Institute for Molecular Biology and Applied Ecology, University of Cagliari, Basilea Pharmaceutica International AG, Jacobs University Bremen, GlaxoSmithKline		\|affiliations = Fraunhofer Institute for Molecular Biology and Applied Ecology, University of Cagliari,<br />Basilea Pharmaceutica International AG, Jacobs University Bremen, GlaxoSmithKline
	\|contact = Email: manfred dot kohler at ime dot fraunhofer dot de		\|contact = Email: manfred dot kohler at ime dot fraunhofer dot de
	\|editors = Baker, Mary		\|editors = Baker, Mary

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	As a compromise for step 1 (Fig. 2), we assembled a collection of user requirement specifications (URS) based on the experiences of one laboratory that had already implemented an ELN. We further selected a small group of super users based on their expertise in documentation processes, representing different wet laboratories and in silico environments. The resulting URS was reviewed by IT and business experts from academic as well as private organisations of the consortium. The final version of the URS is available as Supplemental File 1.		As a compromise for step 1 (Fig. 2), we assembled a collection of user requirement specifications (URS) based on the experiences of one laboratory that had already implemented an ELN. We further selected a small group of super users based on their expertise in documentation processes, representing different wet laboratories and in silico environments. The resulting URS was reviewed by IT and business experts from academic as well as private organisations of the consortium. The final version of the URS is available as Supplemental File 1.

	In parallel, based on literature (Rubacha, Rattan ~~& Hossel~~, ~~2011)~~ and internet searches, presentations of widely used ELNs were evaluated to gain insight into state-of-the-art ELNs. This revealed a wide variety of functional and graphical user interface (GUI) implementations differing in complexity and costs. The continuum between simple out-of-the-box solutions and highly sophisticated and configurable ELNs with interfaces to state-of-the-art analytical tools were covered by the presentations. Notably, the requirements specified by super users also ranged from “easy to use” to “highly individually configurable.” Based on this information, it was clear that the ELN selected for this consortium would never ideally fit all user expectations. Furthermore, the exact number of users and configuration of user groups were unknown at the onset of the project. The most frequently or highest prioritized items of the collected user requirements are listed in Table 2. We divided the gathered requirements into ‘core’ meaning essential and ‘non-core’ meaning ‘nice to have, but not indispensable.’ Further, we list here only the items, which were mentioned by more than two super users from different groups. The full list of URS is available in Supplemental File 1.		In parallel, based on literature<ref name="RubachaAReview11">{{cite journal \|title=A Review of Electronic Laboratory Notebooks Available in the Market Today \|journal=Journal of Laboratory Automation \|author=Rubacha, M.; Rattan, A.K.; Hosselet, S.C. \|volume=16 \|issue=1 \|pages=90–98 \|doi=10.1016/j.jala.2009.01.002}}</ref> and internet searches, presentations of widely used ELNs were evaluated to gain insight into state-of-the-art ELNs. This revealed a wide variety of functional and graphical user interface (GUI) implementations differing in complexity and costs. The continuum between simple out-of-the-box solutions and highly sophisticated and configurable ELNs with interfaces to state-of-the-art analytical tools were covered by the presentations. Notably, the requirements specified by super users also ranged from “easy to use” to “highly individually configurable.” Based on this information, it was clear that the ELN selected for this consortium would never ideally fit all user expectations. Furthermore, the exact number of users and configuration of user groups were unknown at the onset of the project. The most frequently or highest prioritized items of the collected user requirements are listed in Table 2. We divided the gathered requirements into ‘core’ meaning essential and ‘non-core’ meaning ‘nice to have, but not indispensable.’ Further, we list here only the items, which were mentioned by more than two super users from different groups. The full list of URS is available in Supplemental File 1.

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	The issues discussed above also constitute a social or a scientific community problem. Being the first, which often is considered as being the best, is the dictum scientists strive to achieve, especially when performance is reduced to the number of publications and frequency of citation, not to the quality of documentation/reproducibility accounting for determination of quality of results. This culture needs to be replaced by “presenting full sets of high quality results including all metadata” for additional benefit to the scientific community.<ref name="MascarelliResearch14">{{cite journal \|title=Research tools: Jump off the page \|journal=Nature \|author=Mascarelli, A. \|volume=507 \|issue=7493 \|pages=523–5 \|pmid=24678534}}</ref> ELNs could contribute significantly to this goal.		The issues discussed above also constitute a social or a scientific community problem. Being the first, which often is considered as being the best, is the dictum scientists strive to achieve, especially when performance is reduced to the number of publications and frequency of citation, not to the quality of documentation/reproducibility accounting for determination of quality of results. This culture needs to be replaced by “presenting full sets of high quality results including all metadata” for additional benefit to the scientific community.<ref name="MascarelliResearch14">{{cite journal \|title=Research tools: Jump off the page \|journal=Nature \|author=Mascarelli, A. \|volume=507 \|issue=7493 \|pages=523–5 \|pmid=24678534}}</ref> ELNs could contribute significantly to this goal.

			==Discussion==
			We successfully selected and implemented an ELN solution within an ambitiously short timeframe for mostly first-time electronic lab book users. The implementation included the creation and arrangement of internal training material and the establishment of an ELN helpdesk as a SPoC.

			===Lessons learned from the selection and implementation of an ELN solution===
			Generally accepted strategies for software selection and implementation are recommended because they provide a structured and well-defined process for decision-making. Typically, any selection process involves balancing several contrasting features. In our case, the functionality of the system was balanced against long-term maintenance options and costs. The choice was a compromise between these three aspects.

			Performance, ease of use and functionality are the most important aspects for end users of newly launched software. The general expectation is that software should make work quicker, easier and more precise. Thus, users anticipate that software should simplify typical tasks and support their current workflow without adaptation. However, an optimal use of the potential capacity of an ELN requires a change in the working process. Replacing the paper-based LN by a fixed installed lab PC will not lower the entrance barrier. The benefit for the end-user must be communicated in data handling and flexibility in data reuse (off-site use and rapid communication among partners).

			For an ELN in a PPP, the documentation of daily work is the key issue. In particular, in a project with widespread activities ranging from fundamental chemical wet laboratory and in silico work to biological in vitro and in vivo studies, the communication between the sites requires certain data structures. The selected ELN must support many different types of documentation (e.g., flat text files, unstructured images and multidimensional data containers) and in parallel must be at least as flexible as a paper-based notebook (e.g., portable, accessible, ready for instant use and suitable for use when the researcher is wearing laboratory protective clothing). The concealed features of an ELN, such as comprehensive filing of all information for an experiment in one place, standardised structuring of experiments, and long-term global accessibility are not as important for the end user when they are working with the system. The end user requires fast access to his latest experiments and expects support of his specific workflow during documentation. For some users, documenting laboratory work in an electronic system also requires more time and attention than writing entries in a paper notebook.

			No ELN can fully reproduce the flexibility of a blank piece of paper. The first draft for experimental documentation in a classical paper-based LN can be rough and incomplete because only the documenter needs to understand it. Later on, the user can improve the notes and add additional information. In contrast, the documentation process in an ELN is more structured and guided by mandatory fields, which appears to be more time-consuming to the user. However, the overall process could be faster once the user gets familiar with the system. The opportunity to lose any necessary information would be lowered by using the system online during the practical work. There are also other advantages in the ELN, e.g., linking experiments to regular protocols.

			The main value of an ELN is that it makes the data more sharable because it is:

			* constantly accessible;
			* more complete; and
			* easier to follow.

			===Lessons learned from technical solutions===
			Operating system or configuration dependent issues were also encountered frequently. Supporting different systems and browsers, and interfacing with other tools such as office software packages, is complex and requires testing in different environments. Only the most common combinations of systems and tools are recommended by vendors. One possible source of difficulty was the laboratory computers in academia. For the purpose of data recording, older versions of software running on outdated hardware are often used with restrictions based on instrument software installed on them (Supplemental File 2). Many incompatibilities are based on atypical configurations. However, it is impossible to drive the computer upgrade path for laboratory computers from the requirements of a single system, particularly for academic partners. Furthermore, in large academic institutions, many systems are not updated due to frequently changing personnel structures.

			===Data sharing===
			Science, by definition, should be a discipline sharing ”knowledge” with the scientific community and the general public<ref name="DFGProposals13" />, particularly if funded by public organizations. Creating knowledge only for self-interests makes little sense, because knowledge can be verified and extended only by disputation with other researchers. Why do we struggle to share and discuss our data with colleagues?

			Scientists often display a strong unwillingness to share their data. They often believe they are the data owner, i.e., the entity that can authorize or deny access to the data. Nevertheless, they are responsible for data accuracy, integrity and completeness as the representative of the data owner. The data generator should be granted primary use (i.e., publication) of the data<ref name="DFGProposals13" />, but the true owner is the organization that financially supports the project.

			Within a PPP project, it is necessary to establish a documentation policy that is suitable for all. An agreement must occur on standards for the responsibility, content and mechanisms of documentation, particularly in international collaborations where country-specific and cultural differences need to be addressed.<ref name="ElliottWhatAre10">{{cite web \|url=https://www.scientificcomputing.com/article/2010/03/what-are-benefits-eln \|title=What are the Benefits of ELN? \|author=Elliott, M.H. \|work=Scientific Computing \|publisher=Advantage Business Media \|date=30 March 2010}}</ref> Furthermore, no official, widely accepted standards are pre-defined. As long as the justification for ELNs is for more control over performance than to foster willingness to cooperate and share data and knowledge in the early phase of experiments, user acceptance will remain low.<ref name="MyersCollab14" /> Without user acceptance, the quality of the documented work will not improve.<ref name="AsifImproving11">{{cite journal \|title=Improving quality of experimentation procedure through electronic note book (ELN): A qualitative study \|journal=Journal of Quality and Technology Management \|author=Asif, K.H.; Ahsan, S.M.; Aslam, M. \|volume=7 \|issue=2 \|pages=83–90 \|year=2011 \|url=http://pu.edu.pk/images/journal/iqtm/PDF-FILES/05-Improving_Quality_of_Experimentation_Procedure.pdf}}</ref><ref name="ZengImpact11">{{cite journal \|title=Impact of the implementation of a well-designed electronic laboratory notebook on bioanalytical laboratory function \|journal=Bioanalysis \|author=Zeng, J.; Hillman, M.; Arnold, M. \|volume=3 \|issue=13 \|pages=1501–11 \|year=2011 \|doi=10.4155/bio.11.116 \|pmid=21728774}}</ref>

	==References==		==References==

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			===Conclusions from the survey===
			About 40 percent of the users did not find the selected solution appropriate for their specific requirements. Either the solution did not support specific data sets or experiment types, or the solution did not respond fast enough to be used adequately. This indicates that the solution was not fit for purpose. More individual user demands would have to be considered to improve the outcome. This would require more resources in time and manpower than can be accommodated in a publicly funded project. Time would be a key factor as experimental work begins within six months after project kick-off, and the documentation process of experiments starts parallel to the experimental initiation. Keeping in mind that every user needs training time to get acquainted to a new system and there are always initial ‘pitfalls’ to any newly introduced system, an electronic laboratory notebook must be available within four to five months after project start. About one month should be allocated for the vendor negotiation process. Another month or two are required for writing and launching the tender process. This reduces the time frame for a systematic user requirement evaluation process to less than one month after kick-off meeting. It should be acknowledged that not all types of experiments will be fully defined nor will all users be identified. Thus the selection process will always be based on assumptions as described above.

			The slow response of the selected system might have occurred due to many potential issues. It could be related to the bandwidth available at the location, but more frequently we believe this is based on the hardware available. We tested the ELN on modern hardware with low and high bandwidth (Windows: Core i7 CPU @ 2.6 GHz, 6 GB RAM tested on ADSL: 25 kbit/s download, 5 kbit/s upload and iMac Core i5 CPU @ 3.2 GHz, 4 MB RAM tested on ADSL: 2 kbit/s download and 400 bit/s upload) without a major impact on performance, but we did not test old hardware. During this project we learned that in certain labs, computers run Windows XP, MS Office 2003 and Internet Explorer 8. Using outdated software and hardware can be a contributor to the slow response of the ELN. Another potential issue could arise from uploading huge data sets on slow asymmetric digital subscriber lines (ADSL). Users working on local file servers and downloading data from the internet face unexpected low performance when uploading data to a web resource using ADSL, which is due to low upload bandwidth, respectively high latency. This is true for all centralized server infrastructures accessed by internet lines, including SaaS, and should be reflected when considering hosting in the cloud.

			Finally, users demand similar functionalities as on their daily working platform. This is an unsolved challenge due to the heterogeneity of software used in life sciences, from interactive graphical user interface (GUI) based office packages to highly sophisticated batch processing systems. The evolution of new ELNs should provide more closely aligned capabilities to meet the users’ requirements.

			For the ongoing PPP project, a more individualized user support capability may have helped to overcome some of the issues mentioned above. Individual on-site training parallel to the experimental work could offer insight to users’ issues and provide advice for solutions or workarounds. This activity would require either additional travel for a small group of super users or the creation of a larger, widely spread group of well-trained super users which is highly informed about ongoing issues and solutions.

			The issues discussed above also constitute a social or a scientific community problem. Being the first, which often is considered as being the best, is the dictum scientists strive to achieve, especially when performance is reduced to the number of publications and frequency of citation, not to the quality of documentation/reproducibility accounting for determination of quality of results. This culture needs to be replaced by “presenting full sets of high quality results including all metadata” for additional benefit to the scientific community.<ref name="MascarelliResearch14">{{cite journal \|title=Research tools: Jump off the page \|journal=Nature \|author=Mascarelli, A. \|volume=507 \|issue=7493 \|pages=523–5 \|pmid=24678534}}</ref> ELNs could contribute significantly to this goal.

	==References==		==References==

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	Overall, the regular documentation of experiments in the ELN appeared to be unappealing to researchers. This infrequent usage prompted us to carry out a survey of user acceptance in May/June 2015 (detailed description of analysis methods including [[KNIME]] workflow<ref name="BertholdKNIME08">{{cite book \|url=http://www.inf.uni-konstanz.de/bioml2/publications/Papers2007/BCDG+07_knime_gfkl.pdf \|format=PDF \|chapter=KNIME: The Konstanz Information Miner \|title=Data Analysis, Machine Learning and Applications \|author=Berthold, M.R.; Cebron, N.; Dill, F. et al. \|editor=Preisach, C.; Burkhardt, H.; Schmidt-Thieme, L.; Decker, R. \|publisher=Springer-Verlag Berlin Heidelberg \|pages=319–326 \|year=2008 \|isbn=9783540782469 \|doi=10.1007/978-3-540-78246-9}}</ref> and raw data are provided in Supplemental File 2). The primary aim was to evaluate user experiences compared to expectations in more detail. In addition, the administrative team wanted to get feedback to determine what could be done to the existing support structure to increase usage or simplify the routine documentation of laboratory work. Overall, 77 users (see Table 4) were invited to participate in the survey. Two users left the project during the runtime of the survey. We received feedback from 60 (=80%) out of the remaining 75 users. Two questionnaires were rejected due to less than 20% answered questions. The number of evaluated questionnaires is 58 (see Supplemental File 5).		Overall, the regular documentation of experiments in the ELN appeared to be unappealing to researchers. This infrequent usage prompted us to carry out a survey of user acceptance in May/June 2015 (detailed description of analysis methods including [[KNIME]] workflow<ref name="BertholdKNIME08">{{cite book \|url=http://www.inf.uni-konstanz.de/bioml2/publications/Papers2007/BCDG+07_knime_gfkl.pdf \|format=PDF \|chapter=KNIME: The Konstanz Information Miner \|title=Data Analysis, Machine Learning and Applications \|author=Berthold, M.R.; Cebron, N.; Dill, F. et al. \|editor=Preisach, C.; Burkhardt, H.; Schmidt-Thieme, L.; Decker, R. \|publisher=Springer-Verlag Berlin Heidelberg \|pages=319–326 \|year=2008 \|isbn=9783540782469 \|doi=10.1007/978-3-540-78246-9}}</ref> and raw data are provided in Supplemental File 2). The primary aim was to evaluate user experiences compared to expectations in more detail. In addition, the administrative team wanted to get feedback to determine what could be done to the existing support structure to increase usage or simplify the routine documentation of laboratory work. Overall, 77 users (see Table 4) were invited to participate in the survey. Two users left the project during the runtime of the survey. We received feedback from 60 (=80%) out of the remaining 75 users. Two questionnaires were rejected due to less than 20% answered questions. The number of evaluated questionnaires is 58 (see Supplemental File 5).

			{\|
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			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="3"\|'''Table 4.''' Number of users of the ELN and participants in the survey
			\|-
			! style="padding-left:10px; padding-right:10px;"\|Description
			! style="padding-left:10px; padding-right:10px;"\|''n''
			! style="padding-left:10px; padding-right:10px;"\|Remarks
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Maximum number of parallel users of the ELN
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|87
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Number of parallel users at the time point of the survey
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|84
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Administrators
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|3
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Not invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|External reviewers
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|4
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Not invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Project owners = Principal investigators
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|26
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Normal user
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|51
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Deactivated users during the runtime of the questionnaire
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|2
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Questionnaires returned
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|60
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Questionnaires rejected due to insufficient (less than 20%) number of answered questions
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|2
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Evaluated questionnaires
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|58
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\|}
			\|}

	==References==		==References==

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			In an initial analysis, we evaluated user experience by the number of help desk tickets created during the live time of the system (Fig. 4, orange line).

			During the initial phase (2013.06–2013.10) most of the tickets were associated with user access to the ELN. However, after six months (2013.12–2014.01), many requests were related to functionality, especially those from infrequent ELN users. In February 2015, the vendor released an updated graphical user interface (GUI), resulting in a higher number of tickets referring to modified or missing functions and the slow response of the system. The higher number of tickets in August/September 2015 were related to a call for refreshing assigned user accounts. However, overall the number of tickets was within the expected range (<10 per month).

			There was a clear decline in frequent usage during the project runtime. The ELN was officially introduced in June 2013, and the number of experiments increased during the following month as expected (Fig. 4, blue bars). The small decrease in November 2013 was anticipated as a reaction to a new release, which caused some issues on specific operating system/browser combinations and language settings. Support for Windows XP also ended at this time. Some of the issues were resolved with the new release (December 2013). The increase in new experiments in October 2014 and subsequent decline in November 2014 is correlated to a reminder sent out to the members of the project to record all activities into the ELN. The same is true for September/October 2015. The last quarter of each year illustrates year-end activities, including the conclusion of projects and the completion of corresponding paperwork, as reflected in the chart (Fig. 4, orange line).

			Overall, the regular documentation of experiments in the ELN appeared to be unappealing to researchers. This infrequent usage prompted us to carry out a survey of user acceptance in May/June 2015 (detailed description of analysis methods including [[KNIME]] workflow<ref name="BertholdKNIME08">{{cite book \|url=http://www.inf.uni-konstanz.de/bioml2/publications/Papers2007/BCDG+07_knime_gfkl.pdf \|format=PDF \|chapter=KNIME: The Konstanz Information Miner \|title=Data Analysis, Machine Learning and Applications \|author=Berthold, M.R.; Cebron, N.; Dill, F. et al. \|editor=Preisach, C.; Burkhardt, H.; Schmidt-Thieme, L.; Decker, R. \|publisher=Springer-Verlag Berlin Heidelberg \|pages=319–326 \|year=2008 \|isbn=9783540782469 \|doi=10.1007/978-3-540-78246-9}}</ref> and raw data are provided in Supplemental File 2). The primary aim was to evaluate user experiences compared to expectations in more detail. In addition, the administrative team wanted to get feedback to determine what could be done to the existing support structure to increase usage or simplify the routine documentation of laboratory work. Overall, 77 users (see Table 4) were invited to participate in the survey. Two users left the project during the runtime of the survey. We received feedback from 60 (=80%) out of the remaining 75 users. Two questionnaires were rejected due to less than 20% answered questions. The number of evaluated questionnaires is 58 (see Supplemental File 5).

	==References==		==References==

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	• Social networking and collaborative (chat) features<br />		• Social networking and collaborative (chat) features<br />
	• Storage for large sets of “raw” data for re-analysis<br />		• Storage for large sets of “raw” data for re-analysis<br />
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			Based on the user URS, a tender process (Step 2, Fig. 2) was initiated in which vendors were invited to respond via a request for proposal (RFP) process. The requirement of the proposed ELN to support both chemical and biological research combined with the need to access the ELN by different operating systems (Windows, Linux, Mac OS) (see Fig. 3) reduced the number of appropriate vendors. Their response provided their offerings aligned to the proposed specifications.

			Key highlights and drawbacks of the proposed solutions were collected as well as approximations for the number of required licenses and maintenance costs. The cost estimates for licenses were not comparable because some systems require individual licenses whereas others used bulk licenses. At the time of selection, the exact number of users was not available.

			Interestingly, the number of user specifications available out-of-the-box differed by less than 10 percent between systems with the lowest (67) and highest (73) number of proper features. Thus, highlights and drawbacks became a more prominent issue in the selection process.

			For the third step, (Fig. 2), the two vendors meeting all the core user requirements and the highest number of non-core user requirements were selected to provide a more detailed online demonstration of their ELN solution to a representative group of users from different project partners. In addition, a quote for 50 academic and 10 commercial licenses was requested. The direct comparison did not result in a clear winner; both systems included features that were instantly required, but each lacked some of the essential functionalities.

			For the final decision, only features which were different in both systems and supported the PPP were ranked between 1 = low (e.g., academic user licenses are cheap) and 5 = high (e.g., cloud hosting) as important for the project. The decision between the two tested systems was then based on the higher number of positively ranked features, which revealed most important after presentation and internal discussions of super users. The main drivers for the final decision are listed in Table 3. In total, the chosen system got 36 positive votes on listed features meeting all high ranked demands listed in Table 3, while the runner-up had 24 positive votes on features. However, if the system had to be set up in the envisaged consortium it turned out to be too expensive and complex in maintenance.


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			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="1"\|'''Table 3.''' List of drivers for final decision about which ELN solution to be set up and run in the project consortium
			\|-
			! style="padding-left:10px; padding-right:10px;"\|Main drivers for the final decision
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			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			• Many end users were unfamiliar with the use of ELNs, therefore the selected solution should be intuitive<br />
			• Easy to install and maintain<br />
			• Minimal user training required<br />
			• Basic functionalities available out-of-the-box (import of text, spreadsheet, PDF, images and drawing of chemical structures), with as few configurations as possible<br />
			• ELN does not apply highly sophisticated checking procedures, which would require a high level of configuration, restricting users to apply their preferred data format (users should take responsibility for the correct data and the correct format of the data stored in the ELN instead)<br />
			• Web interface available to support all operating systems to avoid deploying and managing multiple site instances<br />
			• Vendor track record—experience of the vendor with a hosted solution as an international provider<br />
			• Sustainability:<br />
			•• affordable for academic partners also after the five year funding duration of the project (based on the maturity of the vendor, number of installations/users, the state-of-the-art user interface and finally also the costs)<br />
			•• easy to maintain (minimal administrative tasks, mainly user management)<br />
			•• support of different, independent user groups<br />
			•• configurable private and public templates for experiments<br />
			• Proposed installation time-frame<br />
			• Per user per year costs for academics and commercial users<br />
			\|-
			\|}
			\|}

			The complete process, from the initial collection of URS data until the final selection of the preferred solution, took less than five months.

			Following selection, the product was tested before specific training was offered to the user community.<ref name="IyerImplem12">{{cite journal \|title=Implementation of an Electronic Lab Notebook to Integrate Research and Education in an Undergraduate Biotechnology Program \|journal=Technology Interface International Journal \|author=Iyer, R.; Kudrle, W. \|volume=12 \|issue=2 \|pages=5–12 \|url=http://tiij.org/issues/issues/spring2012/spring_summer_2012.htm}}</ref> Parallel support frameworks were rolled out at this time, including a help desk as a single point of contact (SPoC) for end users.

			The fourth step (Fig. 2) was the implementation of the selected platform. This deployment was simple and straightforward because it was available as software as a service (SaaS) hosted as a cloud solution. Less than one week after signing the contract, the administrative account for the software was created and the online training of key administrators commenced. The duration of training was typically less than two hours, including tasks such as user and project administration.

			To accomplish step 5 (Fig. 2), internal training material was produced based on the experiences made during the initial introduction of the ELN to the administrative group. This guaranteed that all users would receive applicable training. During this initial learning period, the system was also tested for the requested user functionalities. Workarounds were defined for missing features detected during the testing period and integrated into the training material.

			One central feature of an ELN in its final stage is the standardization of minimally required information. These standardizations include, but are not limited to:

			* Define required metadata fields per experiment (e.g., name of the author, date of creation, experiment type, keywords, aim of experiment, executive summary, introduction).
			* Define agreed naming conventions for projects.
			* Define agreed naming conventions for titles of experiments.
			* Prepare (super user agreed) list of values for selection lists.
			* Define type of data which should be placed in the ELN (e.g., raw data, curated data).

			We did not define specific data formats since we could not predict all the different types of data sets that would be utilized during the lifetime of the ELN. Instead, we gave some best practise advice on arranging data (Supplemental Files 3 and 4), facilitating its reuse by other researchers. The initially predefined templates, however, were only rarely adopted, with some groups using nearly the same structure to document their experiments. More support especially for creating templates may help users to document their results more easily.

			For the final phase, the go live, high user acceptance was the major objective. A detailed plan was created to support users during their daily work with the ELN. This comprised the setup of a support team (the project specific ELN-Helpdesk) as a SPoC and detailed project-specific online training, including documentation for self-training. As part of the governance process, we created working instructions describing all necessary administrative processes provided by the ELN-Helpdesk.

			Parallel to the implementation of the ELN-Helpdesk, a quarterly electronic newsletter was rolled out. This was used advantageously to remind potential users that the ELN is an obligatory central repository for the project. The newsletter also provided a forum for users to access information and news, messaging to remind them the value of this collaborative project.

			Documents containing training slide sets, frequently asked questions (FAQs) and best practice spreadsheet templates (Supplemental File 4) have been made available directly within the ELN to give users rapid access to these documents while working with the ELN. In addition, the newsletter informed all users about project-specific updates or news about the ELN.

			==Results==
			===Operation of the ELN===
			Software operation can be generally split into technical component/cost issues and end-user experiences. The technical component considers stability, performance and maintenance, whereas the end-user experience is based on the capability and usability of the software.

			====Technical solution====
			The selected ELN, hosted as a SaaS solution with a cloud-based service centre, provided a stable environment with acceptable performance, e.g., login <15 sec, opening an experiment with five pages <20 sec (for further technical details, please see Supplemental File 1). During the evaluation period of two years, two major issues emerged. The first involved denial of access to the ELN for more than three hours, due to an external server problem, which was quickly and professionally solved after contacting the technical support, and the other was related to the introduction of a new user interface (see below).

			The administration was simple and straightforward, comprising mainly minor configurations at the project start and user management during the runtime. One issue was the gap in communication regarding the number of active users, causing a steady increase in number of licenses.

			A particular disadvantage using the selected SaaS solution concerned system upgrades. There was little notice of upcoming changes, and user warnings were hidden in a weekly mailing. To keep users updated, weekly or biweekly mails about the ELN were sent to the user community by the vendor. Although these messages were read by users initially, interest diminished over time. Consequently, users were confused when they accessed the system after an upgrade and the functionality or appearance of the ELN had changed. On the other side, system upgrades were performed over weekends to minimize system downtime.

			The costs per user were reasonable, especially for the academic partners for whom the long-term availability of the system, even after project completion, could be assured. This seemed to be an effect of the competitive market that caused a substantial drop in price during the last years.

			====User experience====
			In total, more than 100 users were registered during the first two years runtime, whereas the maximum number of parallel user accounts was 87; i.e., 13 users left the project for different reasons. The number of 87 users is composed of admins (n = 3), external reviewers (n = 4), project owners (n = 26) which are reviewing and countersigning as principal investigators (PIs), and normal users (n = 41). Depending on the period, the number of newly entered experiments per month ranged between 20 and 200 (Fig. 4, blue bars). The size of the uploaded or entered data was heterogeneous and comprised experiments with less than 1 MB, i.e., data from small experimental assays, but also contained data objects much larger than 100 MB, e.g., raw data from mass spectroscopy. Interestingly, users structured similar experiments in different ways. Some users created single experiments for each test set, while other combined data from different test sets into one experiment.

			[[File:Fig4 Vaas PeerJCompSci2016 2.jpg\|800px]]
			{{clear}}
			{\|
			\| STYLE="vertical-align:top;"\|
			{\| border="0" cellpadding="5" cellspacing="0" width="800px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\| <blockquote>'''Figure 4.''' Overview of usage of the ELN and workload for the helpdesk over time:
			Y-axis on the left shows number of experiments created per month (blue bars) overlaid by number of help desk tickets created per month (orange line) scaled on the y-axis on the right.</blockquote>
	\|-		\|-
	\|}		\|}
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	==Notes==		==Notes==
	This presentation is faithful to the original, with only a few minor changes to presentation, including regionalizing spelling. In some cases important information was missing from the references, and that information was added. The original lists references in alphabetical order; this version lists them in order of appearance due to the nature of the wiki.		This presentation is faithful to the original, with only a few minor changes to presentation, including regionalizing spelling. In some cases important information was missing from the references, and that information was added. The original lists references in alphabetical order; this version lists them in order of appearance due to the nature of the wiki. Supplemental file names have been clarified in the text.

	<!--Place all category tags here-->		<!--Place all category tags here-->

Shawndouglas: Saving and adding more.

2017-09-12T17:28:55Z

Saving and adding more.

← Older revision		Revision as of 17:28, 12 September 2017
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	In this article we describe the process of selecting and implementing an ELN in the context of the multisite PPP project TRANSLOCATION, comprising about 90 bench scientists in total. Furthermore we present the results from a survey evaluating the users’ experiences and the benefit for the project two years post-implementation. Based on our experiences, the specific needs in a PPP setting are summarized and lessons learned will be reviewed. As a result, we propose recommendations to assist future users avoiding pitfalls when selecting and implementing ELN software.		In this article we describe the process of selecting and implementing an ELN in the context of the multisite PPP project TRANSLOCATION, comprising about 90 bench scientists in total. Furthermore we present the results from a survey evaluating the users’ experiences and the benefit for the project two years post-implementation. Based on our experiences, the specific needs in a PPP setting are summarized and lessons learned will be reviewed. As a result, we propose recommendations to assist future users avoiding pitfalls when selecting and implementing ELN software.

			==Methods==
			===Selection and implementation of an ELN solution===
			The IMI project call requested a high level of transparency enabling the sharing of data to serve as an example for future projects. The selected consortium TRANSLOCATION had a special demand for an ELN due to its structure — various labs and partners spread widely across Europe needed to report into one common repository — and due to the final goal, data was required to be stored and integrated into one central information hub, the ND4BB Information Centre. Fortunately, no legacy data had to be migrated into the ELN.

			The standard process for the introduction of new software follows a highly structured multi-phase procedure<ref name="NehmeElect06">{{cite book \|chapter=9. Electronic Laboratory Notebooks \|title=Computer Applications in Pharmaceutical Research and Development \|author=Nehme, A.; Scoffin, R.A. \|editor=Ekins, S.; Wang, B. \|publisher=Wiley \|year=2006 \|pages=209–27 \|isbn=9780471737797}}</ref><ref name="MilstedLabTrove13">{{cite journal \|title=LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory \|journal=PLoS One \|author=Milsted, A.J.; Hale, J.R.; Grey, J.G.; Neylon, C. \|volume=8 \|issue=7 \|pages=e67460 \|year=2013 \|doi=10.1371/journal.pone.0067460 \|pmid=23935832 \|pmc=PMC3720848}}</ref>, as outlined in Fig. 2.


			[[File:Fig2 Vaas PeerJCompSci2016 2.jpg\|500px]]
			{{clear}}
			{\|
			\| STYLE="vertical-align:top;"\|
			{\| border="0" cellpadding="5" cellspacing="0" width="500px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\| <blockquote>'''Figure 2.''' Schematic outline of stepwise procedure for the implementation of a new system<ref name="NehmeElect06" /></blockquote>
			\|-
			\|}
			\|}

			For the first step, we had to manage a large and highly heterogeneous user group (Fig. 3) that would be using the ELN, scheduled for roll-out within six months after project launch. All personnel of the academic partners were requested to enter data into the same ELN, potentially leading to unmet individual user requirements, especially for novices and inexperienced users.

			[[File:Fig3 Vaas PeerJCompSci2016 2.jpg\|500px]]
			{{clear}}
			{\|
			\| STYLE="vertical-align:top;"\|
			{\| border="0" cellpadding="5" cellspacing="0" width="500px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\| <blockquote>'''Figure 3.''' Technical and organizational challenge: schematic overview of paths for sharing research activity results within a public–private partnership on antimicrobial research</blockquote>
			\|-
			\|}
			\|}

			As a compromise for step 1 (Fig. 2), we assembled a collection of user requirement specifications (URS) based on the experiences of one laboratory that had already implemented an ELN. We further selected a small group of super users based on their expertise in documentation processes, representing different wet laboratories and in silico environments. The resulting URS was reviewed by IT and business experts from academic as well as private organisations of the consortium. The final version of the URS is available as Supplemental File 1.

			In parallel, based on literature (Rubacha, Rattan & Hossel, 2011) and internet searches, presentations of widely used ELNs were evaluated to gain insight into state-of-the-art ELNs. This revealed a wide variety of functional and graphical user interface (GUI) implementations differing in complexity and costs. The continuum between simple out-of-the-box solutions and highly sophisticated and configurable ELNs with interfaces to state-of-the-art analytical tools were covered by the presentations. Notably, the requirements specified by super users also ranged from “easy to use” to “highly individually configurable.” Based on this information, it was clear that the ELN selected for this consortium would never ideally fit all user expectations. Furthermore, the exact number of users and configuration of user groups were unknown at the onset of the project. The most frequently or highest prioritized items of the collected user requirements are listed in Table 2. We divided the gathered requirements into ‘core’ meaning essential and ‘non-core’ meaning ‘nice to have, but not indispensable.’ Further, we list here only the items, which were mentioned by more than two super users from different groups. The full list of URS is available in Supplemental File 1.

			{\|
			\| STYLE="vertical-align:top;"\|
			{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="70%"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="2"\|'''Table 2.''' Overview of user requirements organized as ‘core user requirements’ for essential items, and ‘non-core user requirements’ representing desirable features
			\|-
			! style="padding-left:10px; padding-right:10px;"\|Core user requirements
			! style="padding-left:10px; padding-right:10px;"\|Non-core user requirements
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			• System set-up and implementation should be fast and simple<br />
			• Access from different platforms should be possible: Windows, Linux, Mac OS<br />
			• Low training requirements (for high level of acceptance<br />
			• Hosted system with state-of-the-art security settings<br />
			• Simple user management (only limited support by project members possible)<br />
			• Suitable for both chemical (including e.g., drawings of molecules) and biological (including e.g., capture fluorescent images) experiments<br />
			• Low costs, especially for long-term usage in the academic area<br />
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			• Conform with Good Laboratory Practise<br />
			• User management with dedicated access permissions (expectation: all users working on the same project, but in different work packages)<br />
			• Workflow management<br />
			• Order management<br />
			• Chemical structure handling<br />
			• Dedicated tree structure for storing experiments<br />
			• Legally-binding procedures (signatures)<br />
			• Modular expandability<br />
			• Appropriate integrated analytical features<br />
			• Social networking and collaborative (chat) features<br />
			• Storage for large sets of “raw” data for re-analysis<br />
			\|-
			\|}
			\|}

	==References==		==References==

← Older revision		Revision as of 19:16, 12 September 2017
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	Overall, the regular documentation of experiments in the ELN appeared to be unappealing to researchers. This infrequent usage prompted us to carry out a survey of user acceptance in May/June 2015 (detailed description of analysis methods including [[KNIME]] workflow<ref name="BertholdKNIME08">{{cite book \|url=http://www.inf.uni-konstanz.de/bioml2/publications/Papers2007/BCDG+07_knime_gfkl.pdf \|format=PDF \|chapter=KNIME: The Konstanz Information Miner \|title=Data Analysis, Machine Learning and Applications \|author=Berthold, M.R.; Cebron, N.; Dill, F. et al. \|editor=Preisach, C.; Burkhardt, H.; Schmidt-Thieme, L.; Decker, R. \|publisher=Springer-Verlag Berlin Heidelberg \|pages=319–326 \|year=2008 \|isbn=9783540782469 \|doi=10.1007/978-3-540-78246-9}}</ref> and raw data are provided in Supplemental File 2). The primary aim was to evaluate user experiences compared to expectations in more detail. In addition, the administrative team wanted to get feedback to determine what could be done to the existing support structure to increase usage or simplify the routine documentation of laboratory work. Overall, 77 users (see Table 4) were invited to participate in the survey. Two users left the project during the runtime of the survey. We received feedback from 60 (=80%) out of the remaining 75 users. Two questionnaires were rejected due to less than 20% answered questions. The number of evaluated questionnaires is 58 (see Supplemental File 5).		Overall, the regular documentation of experiments in the ELN appeared to be unappealing to researchers. This infrequent usage prompted us to carry out a survey of user acceptance in May/June 2015 (detailed description of analysis methods including [[KNIME]] workflow<ref name="BertholdKNIME08">{{cite book \|url=http://www.inf.uni-konstanz.de/bioml2/publications/Papers2007/BCDG+07_knime_gfkl.pdf \|format=PDF \|chapter=KNIME: The Konstanz Information Miner \|title=Data Analysis, Machine Learning and Applications \|author=Berthold, M.R.; Cebron, N.; Dill, F. et al. \|editor=Preisach, C.; Burkhardt, H.; Schmidt-Thieme, L.; Decker, R. \|publisher=Springer-Verlag Berlin Heidelberg \|pages=319–326 \|year=2008 \|isbn=9783540782469 \|doi=10.1007/978-3-540-78246-9}}</ref> and raw data are provided in Supplemental File 2). The primary aim was to evaluate user experiences compared to expectations in more detail. In addition, the administrative team wanted to get feedback to determine what could be done to the existing support structure to increase usage or simplify the routine documentation of laboratory work. Overall, 77 users (see Table 4) were invited to participate in the survey. Two users left the project during the runtime of the survey. We received feedback from 60 (=80%) out of the remaining 75 users. Two questionnaires were rejected due to less than 20% answered questions. The number of evaluated questionnaires is 58 (see Supplemental File 5).

			{\|
			\| STYLE="vertical-align:top;"\|
			{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="70%"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" colspan="3"\|'''Table 4.''' Number of users of the ELN and participants in the survey
			\|-
			! style="padding-left:10px; padding-right:10px;"\|Description
			! style="padding-left:10px; padding-right:10px;"\|''n''
			! style="padding-left:10px; padding-right:10px;"\|Remarks
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Maximum number of parallel users of the ELN
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|87
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Number of parallel users at the time point of the survey
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|84
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Administrators
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|3
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Not invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|External reviewers
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|4
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Not invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Project owners = Principal investigators
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|26
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Normal user
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|51
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Invited to participate in survey
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Deactivated users during the runtime of the questionnaire
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|2
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Questionnaires returned
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|60
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Questionnaires rejected due to insufficient (less than 20%) number of answered questions
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|2
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|Evaluated questionnaires
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|58
			\| style="background-color:white; padding-left:10px; padding-right:10px;"\|
			\|-
			\|}
			\|}

	==References==		==References==