Five Benefits of a Cloud ELN

WHITE

PAPER

Five Benefits of a Cloud ELN

Introduction
Recent trends in the pharmaceutical and biotechnology industries 
have influenced to the evolution of electronic lab notebooks (ELN). 
Trends including IT budget allocations and an acceleration of 
outsourcing efforts have resulted in data collaboration beyond 
institutional boundaries. In addition, the efficient collection and 
security of ever growing volumes of data is more essential than 
ever given the realization that “Big Data” significantly improves 
the speed and outcomes of clinical development. 

The implementation of an ELN has a transformative effect on the 
way research is conducted. Beyond ensuring that the needs of 
scientists are met with capabilities specialized for their discipline, 
the business needs to examine factors such as streamlining 
implementation and system costs. R&D organizations that adopt  
a cloud ELN can take advantage of immediate and long-term 
benefits. Cloud-native ELNs delivered as SaaS (software as a 
service) platforms enable scientists of all disciplines to easily 
document and find their work, collaborate within and across 
organizations, as well as enable IT to take advantage of more 
efficient, cost effective storage and performance with automatic 
updates and connectivity to other informatics platforms. In 
addition to the five core benefits cited below, cloud ELNs can be 
deployed quickly (environments can literally be set up in minutes), 
and have high adoption rates and a lower learning curve because 
of their browser-based, modern user experiences. This whitepaper 
will cover a blueprint to identify and expand on these benefits 
that impact both R&D organizations and individual users the most.

Benefit 1 – Improved Collaboration 
Scientific collaboration is more strikingly prevalent today than  
decades ago.1 The trend in many areas of research is toward 
catalyzing collaborative efforts that bring together researchers with 
diverse scientific backgrounds. These alternate perspectives help 
address perplexing questions and solve complex problems that 
benefit from an interdisciplinary or multidisciplinary approach.2

Collaboration is central in your organization and can occur 
internally as well as with external commercial partners or 
academical institutes. The most important aspect of any 
collaboration is the value recognized upon the sharing of data, 
the fuel that powers your research. A siloed, disconnected 
informatics environment creates challenges in project 
management, reporting, and scientific data exchange that  
must be addressed if the team is to collaborate effectively  
and achieve business goals.

In absence of an ELN as a central data repository, research data 
and interpretations are shared in a non-confidential way- often 
via email. Using an ELN to facilitate the sharing of data is more 
efficient and secure, as a consortium of collaborators can define 
who has access to which data while the data continues to be 
stored in a secure environment. Collaboration internal to an R&D 
organization may be as simple as being able to link experiments 
or allowing multiple people to contribute to or comment on  

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the same work. Collaboration can also be more comprehensive. 
For example, you may require an ELN to facilitate how projects 
are spun up and down, how external partners access project-
related reports and documents, and how they communicate  
and share experimental data. It is imperative to define how to 
manage different types of data and data formats such as 
chemical structure and quality data, calculated and measured 
physicochemical properties, biological assay data and pre-clinical 
data describing the characteristics of active pharmaceutical 
ingredients across the partner landscape. In addition, there is  
the consideration of how to distribute and archive the data 
among partners when a project ends. Lastly, and arguably  
most important, how the IP is managed throughout the duration 
of the collaboration must be considered from the start. The 
immense challenge of data management and technology 
exchange becomes most apparent when one considers that a 
typical external collaboration can generate tens of thousands  
of data points throughout its duration.

With these challenges in mind, R&D organizations with many 
partnerships are turning to cloud-native collaboration workspaces 
that are accessible from anywhere with an internet connection and 
provide a level of business agility and security that is not available 
with server-based, on-premise ELNs.

Benefit 2 - Connectivity
ELNs are the heart of scientific data documentation, processing, 
and compliance. At their simplest, they facilitate the capture of 
data and documentation of experiments. At their best, they  
assist the scientist and the business at every step of data 
generation and analysis along the R&D value chain and facilitate 

collaboration with external partners. ELNs that are easily accessible 
and designed to be the central integration point in the informatics 
electronic lab environment will provide the most value. 

As previously mentioned, research is ever more distributed,  
and scientists need to be able to access their information from 
many different locations at any time of day and potentially from 
different machines. Access to a cloud ELN is only limited by 
internet connection. As there is no application installed on the 
machine itself, scientists can review and enter data from any 
internet connected device. Cloud ELNs effectively allow scientists 
to work from anywhere and the heightened connectivity will 
improve efficiency and productivity. 

In addition to better connectivity to the ELN platform itself, there 
is also the benefit of improved connectivity to other informatics 
systems. Scientists, regardless of their discipline, use many 
applications and tools essential to executing their daily work, 
and often the data generated from these other tools need to be 
incorporated into their experiments. Not only is the enterprise 
software landscape of internal systems strikingly different from 
one organization to the next, but there are also external systems 
to consider. Internal systems that the ELN may be required to 
integrate with can include, but is not limited to, chemical and 
biological registration and inventory applications, and laboratory 
information management systems (LIMS). In addition, valuable 
external databases exist with information on available chemicals, 
reaction planning, safety data, and sequence information etc. 
There is also the possible need to connect to digitized equipment 
including balances, pH meters, bioreactors or analytical instruments. 

Figure 1. Intuitive collaboration in Signals Notebook: add comments, tag colleagues and use hashtags to link to relevant experiments.

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Figure 2. Integration of Signals Notebook with ChemACX gives scientists immediate access to pertinent data around commercial availability of materials.

Cloud based ELNs are commonly built off RESTful API’s which 
facilitate data trafficking between disparate systems. Using  
such modern standards for API development, the programmatic 
burden of integrating systems is significantly reduced. Integrations 
can access the APIs of an ELN by an external application to 
precipitate events such as automatically writing instrument data 
to an experiment. Alternatively, a service within the ELN can 
access a third-party API to access stored data about a sample 
from a LIMS or to check the safety and regulatory profile of a 
reagent from an external database. Whichever integrations are 
achieved, the greater agility offered by such modern applications 
allows the ELN to expand to provide the core of a connected 
electronic lab environment.

Cloud ELNs have enhanced connectivity that is inherent in the 
way they are designed and provisioned. There is no “one size  
fits all” ELN, therefore integration with other systems must be 
not only possible, but also streamlined. 

Benefit 3 - Performance at Scale
Whether you’re a scientist, the head of IT, or an investor, you 
can benefit from the exceptional performance of enterprise 
software. An ELN user must be able to upload all different types 
data, quickly find historical data, and have access to the most 
modern, up-to-date functionality in a timely manner. The 
business supporting the ELN will be concerned with ease of 

implementation, accessibility or uptime, and scalability. Cloud 
ELNs fulfill all these needs as they are delivered in a matter of 
minutes, elastically scalable, updated automatically, and have 
guaranteed uptime. 

A well-designed cloud-native ELN will be built on modern 
technology that on-premise ELNs cannot take advantage of. The 
architecture of traditional on-premise ELNs are either a single 
application process or a multi-tiered system of database, web 
server, and application tiers. A cloud-hosted solution of a 
traditional ELN is the same tiered architecture, just installed in 
the cloud. Both have upper performance limits and require 
additional cost, support, or services from IT to analyze the 
system and optimize it in order to scale. In contrast, a well-
designed cloud-native ELN is built with a microservice based 
architecture, meaning each dedicated component can operate 
independently. If one component temporarily fails, others remain 
unaffected and the system is still usable. Microservices are 
resilient and self-healing. They are designed to auto recover from 
adverse events that may impact the database, application servers, 
or network services. This architectural approach has many other 
benefits, including immediate scalability during periods of rapid 
growth, and unrivaled search performance through hundreds of 
millions of entries thanks to modern storage and indexing 
technologies. This is simply not possible with an on-premise or 
cloud-hosted ELN built with traditional architecture.

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Figure 3. Benefits of a microservice architecture: services operate independently and utilization of best-of-breed for each type of technology.3

Cloud ELNs delivered as a SaaS solution also have the advantage 
of elimination of “environmental” issues as well as a continuous 
release cycle that allows the pushing of new functionality 
frequently and, depending on the deployment, automatically. A 
well designed SaaS offering will allow internal administrators to 
configure their own unique workflows that are not impacted by 
these updates. Cloud ELNs also have guaranteed uptime, as the 
entire system is in a controlled environment and is not at the 
mercy of the many variables on-premise systems are. 

Benefit 4 - Security
Protecting and securing your data is paramount. Often at larger 
institutions, entire teams are devoted to doing just that. Of 
course, this includes the data you generate in-house at your 
organization, but 25% of Pharma and Biotech work is  
now outsourced. Data needs to flow into and out of your 
organization every day and the right people need to see the 
right information on-demand.

As data storage in the cloud is elastically scalable, cloud ELNs 
can be automatically backed up daily and those backups can be 
stored for an extended period. Organizations that implement a 
well-designed cloud ELN will benefit from business continuity 
and a disaster recovery plan that has been vetted by a large 
number of customers, as opposed to an on-premise system that 
may have less scrutiny.  

Not only are there multiple copies of your data at any given  
time at one data center, but cloud ELNs also provide the benefit 
of data redundancy. Current best practice for cloud ELN 
infrastructure is to have it deployed and maintained in at least 
two physical and geographic locations to mirror your data and 
guarantee maximum availability if hardware or network issues 
were to occur. In the incredibly unlikely event that a disaster 
occurs at one data center, the other can continue delivering  
the ELN service without interruption or loss of data. 

Cloud ELNs often have several deployment models that can 
include multi-tenant and private cloud environments. A cloud 
vendor should ensure security infrastructure is equally robust, 
regardless of deployment model, though the perception that 
private cloud offerings have better security often leads 
organizations to that option. Regardless of the deployment 
model, data is always encrypted in transit to and from the cloud 
as well as when it is “at rest” in the system. With any cloud 
platform, the vendor should ensure access to the system is based 
on a well-defined role based policy, such that designated people 
only have access to particular subsystems and conduct regular 
proactive security assessments at the network, host, and 
application level, remediating all vulnerabilities in a timely fashion.

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Benefit 5 – Total Cost of Ownership
In the late 1980s, Gartner popularized the term “total  
cost of ownership” (TCO) to define the long-term cost of 
maintenance in addition to the upfront capital investment 
in enterprise technology. It is imperative to consider what 
total cost of ownership means when selecting an electronic 
laboratory notebook for your R&D organization and how it 
could influence your decision. The component most 
people are typically concerned about is the initial capital 
investment required when selecting and implementing a 
solution. Let’s say your organization has reviewed multiple 
vendors for their functional capabilities and the scientists 
are satisfied with the technical aspects. Next, you begin to 
evaluate the costs. 

The complexity of the underlying IT infrastructure and 
maintenance for a cloud ELN as a service, is all handled by 
your cloud ELN vendor. Neither the end users or your 
organization’s IT department must worry about hardware 
maintenance, upgrades to the application, or what versions 
of underlying databases are compatible etc. A cloud ELN is 
managed by the vendor experts who developed and 
understand the application inside and out. They are familiar 
with all operations of the application and can make changes 
to the cloud deployment to ensure maximum levels of 
performance and robustness. Cloud ELNs are quickly scalable 
and can grow with your organization as capacity needs 
increase. With most traditional software, you are not 
guaranteed on how well it will perform when installed on 
your local infrastructure given all the variables at play 
(database, servers, network, end user machines, etc.). With  
a cloud ELN you are, and most vendors will guarantee that 
your application will be up and available 99% of the time.

As mentioned previously, cloud ELNs eliminate the cost for 
data backup, redundancy and recovery because these costly 
and timely services are provided by the ELN vendor, but 
they also eliminate sunken opportunity cost. Cloud ELNs 
can be updated more frequently because everyone is on 
the same source code and vendors don’t have to release 
unique fixes for highly customized ELNs. These more 
frequent updates ensure that the functionality continues  
to be improved and modernized. Cloud ELNs also provide 
the benefit of predictable costs for both licenses and 
administration. Licenses are typically sold as yearly 
subscriptions, so during periods of rapid growth you  
will have a clear idea of what your costs will be. 

Talk about performance! Sub-second structure 
searching in PerkinElmer’s Signals™ Notebook 

Chemical substructure and similarity searching is the 
cornerstone of most cheminformatics systems and a 
critical feature in electronic lab notebooks. However,  
as the scale of cheminformatics systems has grown, 
scientists are often frustrated with the performance of 
their chemical queries. Mature ELNs in production for  
well over a decade at global pharmaceutical and chemical 
companies currently store tens of millions of chemical 
structures and reactions.

PerkinElmer has been the industry leader in adopting 
modern NoSQL technologies to build the next generation 
cloud-native ELN and scientific computing platform, Signals™ 
Notebook. Chemical structure searching in Signals™ 
Notebook is facilitated by PerkinElmer’s ChemSearch NoSQL 
chemistry cartridge, the first chemical search cartridge 
compatible with scalable, NoSQL systems. ChemSearch 
offers exact, substructure, and similarity search capabilities 
with performance at scale. This new search engine is based 
on the open source and battle-tested Elastic Search 
technology- the search engine used by most online 
shopping, airline, hotel reservation, and social media sites. 
Elastic Search is an index, not a database, that consumes 
documents and other electronic content, parses it, and 
organizes it in a way that makes it easier to find. 

PerkinElmer instructed Elastic Search how to perform 
chemical searching and now ChemSearch allows Signals 
Notebook to provide sub-second response time on 
databases with hundreds of millions of molecules and 
reactions. Indexing systems are also very efficient at 
assigning relevance to results, as it is not enough to return 
results quickly. The results must be valid, and the most 
important ones should be returned first. The second step 
in chemical searching is to evaluate which of the screened 
molecules is really a valid substructure of the query 
molecule. This is a complex and computationally expensive 
process akin to a pass/fail relevance test. Matching 
molecules are assigned a high relevance, failing ones are 
dropped from the list of results. The good news again, is 
that Elastic Search is particularly well suited to scoring the 
results via a relevance function. It efficiently parallelizes the 
scoring process by allowing hundreds or even thousands 
of small computers to each handle a fraction of the results 
to score. The net result is a system that is vastly more 
scalable and performant than older SQL Cartridges found 
in many on-premise ELNs.  

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Conclusion
A successful ELN implementation must meet the criteria of and 
provide benefits to both the technical and business sponsors.  
The ELN must enable scientists to quickly and easily narrate their 
experiments, enter and analyze data, and more importantly, 
share and collaborate on that data to move projects forward. 
Project managers should be able to track experiment and project 
progress and gauge efficiency. Investing in a cloud ELN will kick-
start your organization's digital transformation, lower the barrier 
for cross institutional collaboration, and increase R&D efficiency. 

PerkinElmer Signals™ Notebook is the next generation cloud  
ELN and scientific collaboration platform for today’s scientists. 

One of the most intuitive ELNs on the market, it looks and feels 
like modern consumer apps used every day. Signals Notebook 
employs a cloud-based micro-service architecture with advanced 
data lake storage technologies for document storage and indexing. 
PerkinElmer has architected Signals Notebook to grow with 
organization’s needs and is quickly scalable. Collaboration is 
supported with social media-like commenting and notifications 
and creating contextual relationships between experiments. 
Signals Notebook is a SaaS ELN and as such PerkinElmer owns  
all the system maintenance and updates, which deliver new 
functionality and bug fixes every 3-6 weeks. 

Signals Notebook is the intuitive, searchable, scalable, 
and secure platform designed to increase productivity, 
enhance collaboration, and reduce risk. Request your 
30-day free trial today and get started using it 
tomorrow to see for yourself. 

ChemDraw, the world’s leading chemical drawing 
software, is embedded in Signals Notebook for 
seamless support of synthetic chemistry workflows 
and reaction planning.

More About Signals Notebook, Cloud ELN 

Quickly document your procedures and protocols by 
using quick keys to insert auto-text snippets and lists, 
as well as materials or reaction properties linked to the 
stoichiometry grid.

Signals Notebook’s intuitive user experience enables rapid user adoption – get your organization up and running in no time with an ELN 
that looks and feels like modern consumer applications. 

For a complete listing of our global offices, visit www.perkinelmer.com/ContactUs

Copyright ©2018, PerkinElmer, Inc. All rights reserved. PerkinElmer® is a registered trademark of PerkinElmer, Inc. All other trademarks are the property of their respective owners.

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PerkinElmer, Inc. 

940 Winter Street 

Waltham, MA 02451 USA 

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References

1.  Wutchy, S., Jones, B. F., & Uzzi, B. (2007, May 18). The increasing dominance of teams in production of knowledge. Science, 

1036-1039.

2.  Weeks, W. B., Wallace, A. E., & Kimberly, B. C. (2004, Nov). Changes in authorship patterns in prestigious US medical journals. 

Social science & medicine, 1949-1954.

3. Image adapted from https://msdn.microsoft.com/en-us/magazine/mt595752

Signals Notebook has many capabilities to facilitate 
collaboration within and across organizations. 
Teamwork is instantaneous with social media like 
commenting, the ability to link multiple experiments 
and notifications delivered in app or via email. 

Searching has never been faster or easier. With  
syntax free text and property search and proprietary 
ChemSearch functionality for structure searching, 
Signals Notebook delivers the exceptional search 
experience scientists can’t live without.