David Prior, Author at Pistoia Alliance

Pistoia Alliance’s UDM team release first file format specification for chemical reaction information exhange

Posted on 28 June 2018 by David Prior

The Unified Data Model team is delighted to announce the first release of the now-open UDM file format specification which will facilitate the exchange of information about chemical reactions. The new update consists of a definition of the UDM file format (as an XML schema document), several sample datasets (a big “thank you” to Elsevier and InfoChem), and sample source code (in Python and Java) that demonstrate the conversion to the UDM file format and validation of UDM files.

The original unified representation of chemical reactions was co-developed by Elsevier and Roche with contributions from other pharmaceutical companies. It was donated to The Pistoia Alliance in 2017 with the aim of extending the model to support additional requirements, and to increase its adoption as a vendor-agnostic experimental reaction/data format standard.

The current release is compatible with the original version created by Elsevier; it will remove the previous uncertainty around the units of measurement used for individual numerical values and documents fundamental entities.

The project team is continuing to work on a next version of the UDM, which will introduce several enhancements needed for better representation of experiments captured in electronic laboratory notebooks (ELNs). We are grateful to the entire project team for their contributions and to our funders (BIOVIA, Elsevier, GSK, Novartis, Roche) who helped to make this first milestone happen.

72% of Life Science Professionals Believe Their Industry is Behind in the Development of AI, Finds Survey from The Pistoia Alliance

Posted on 7 June 2018 by David Prior

Life science professionals highlight technology and healthcare as collaboration priorities for ensuring successful application of AI

Boston, 7^th June, 2018: A survey of 229 life science professionals from The Pistoia Alliance, a global, not for profit alliance that works to lower barriers to innovation in life sciences R&D, has found the majority (72%) believe their sector is lagging behind other industries in its development of AI. To accelerate the successful use of AI, The Pistoia Alliance has launched its Centre of Excellence for AI in Life Sciences, aiming to encourage greater collaboration between stakeholders to bridge the gap between technology and science. By bringing together best practice, adoption strategy, events, and hackathons covering a range of challenges, the Centre of Excellence will provide a virtual and physical co-working space, enabling life science professionals to learn how best to apply AI, machine, and deep learning to R&D.

The survey found adoption of AI is high, with more than two thirds (69%) of companies using AI, machine learning, deep learning, and chatbots; an increase from when the same question was asked in September 2017, where under half (44%) of respondents were using or experimenting with AI. A further 19% of respondents signalled that they plan to use AI within the next 12 months, with just 12% of life science professionals not using AI at all. Of those currently using AI in their organisations, approximately a fifth (21%) felt that their projects were not yet providing meaningful outcomes, and 21% ‘didn’t know’ if projects were delivering meaningful outcomes. The Pistoia Alliance believes collaboration between interested parties will be essential in ensuring AI projects lead to results that positively impact R&D.

“This survey shows interest in AI remains strong, but there is still a challenge with moving past the hype to a realty where AI is delivering insights with the power to truly augment researchers’ work,” commented Dr Steve Arlington, President of The Pistoia Alliance. “It is significant that a majority of people in our own industry believe we are trailing other sectors in the use of AI, and we must address this issue by working closely with each other and with stakeholders in other sectors. Spaces to virtually collaborate, like our Centre of Excellence, will become even more critical as political and social shifts – from Brexit to changes to US immigration laws – impact how scientists share knowledge and ideas. AI is poised to have a radical impact on life sciences and healthcare, but the industry must give researchers the best chance of success.”

When respondents were asked which sector their primary collaborations will focus on in the next 18 months, the majority said with a technology or data provider (40%). This is an encouraging finding given that access to quality data is crucial to supporting AI; moreover, learning how to build and test algorithms will be a key factor in producing meaningful outcomes from AI projects. This was followed by healthcare (22%), academia (15%), and the government and public sector (4%) – indicating the range of industries that life science companies will need to work with to realise AI’s potential. The Centre of Excellence aims to help facilitate these collaborations by allowing companies to share their expertise and knowledge, in addition to holding events that help organisations build prototypes and pilots that prove the value of AI.

“AI is a multidisciplinary field that needs many inputs to make it effective, and we often hear from our members that making links with other industries, such as the technology sector, is a barrier to AI’s evolution,” commented Dr Nick Lynch, Cofounder of The Pistoia Alliance. “Additionally, there are many concerns around whether AI will ‘take’ our jobs, and how we can ensure AI is ethical and unbiased. The Centre of Excellence will tackle these issues and more through other events and further research, helping researchers understand how AI will augment their work and the role of AI as a fundamental building block in building the Lab of the Future. Ultimately, patients’ lives depend on making breakthroughs, and we encourage anyone interested in AI to get involved with our Centre of Excellence.”

The survey of 229 senior pharmaceutical and life science leaders was conducted via webinar in May 2018. For information and slides from the webinars, see here. To find out how to get involved in the Centre of Excellence for AI in Life Sciences, which is also open to non-member of The Pistoia Alliance, see here.

— ENDS –72% of Life Science Professionals Believe Their Industry is Behind in the Development of AI, Finds Survey from The Pistoia Alliance

About The Pistoia Alliance

The Pistoia Alliance is a global, not-for-profit members’ organization made up of life science companies, technology and service providers, publishers, and academic groups working to lower barriers to innovation in life science and healthcare R&D. It was conceived in 2007 and incorporated in 2009 by representatives of AstraZeneca, GSK, Novartis and Pfizer who met at a conference in Pistoia, Italy. Its projects transform R&D through pre-competitive collaboration. It overcomes common R&D obstacles by identifying the root causes, developing standards and best practices, sharing pre-competitive data and knowledge, and implementing technology pilots. There are currently over 80 member companies; members collaborate on projects that generate significant value for the worldwide life sciences R&D community, using the Pistoia Alliance’s proven framework for open innovation.

HELM adopters – an ever-increasing community

Posted on 24 April 2018 by David Prior

It is easy to be preoccupied with the day-to-day tasks of a project, particularly when development work is progressing full pace. However, it is interesting to look more widely and consider the impact our work has had on the scientific community.

HELM was released in 2013, with a single user – Pfizer (who invented it), but were shortly followed by ChemAxon and a steady stream of organisations which represent a wide section of the informatics community. We have also gained recognition from regulators who endorsed HELM as an acceptable format in ISO 11238.

The list of HELM users is now very healthy, and we appreciate our enthusiastic and engaged community. Here are some of the groups who are using HELM.

Many of the HELM users will be discussing their implementations at the upcoming CINF symposium at the ACS Boston meeting 19-23^rd August. This will be an excellent opportunity to find out the latest information from those working in the field.

Pharma/Biotech

Novartis:

Novartis makes extensive use of HELM for nucleotide registration and analysis. The open-source HELM tools are integrated with the internal informatics landscape.

Yohann Potier said, “HELM allows Novartis to accurately describe its chemically-modified constructs using an industry standard for registration.”

Pfizer:

As the originators of the HELM standard, Pfizer has based their entire macromolecular registration infrastructure on HELM and its associated biomolecule toolkit.

Sergio Rotstein said, “While the enablement of biomolecular registration was already of great value to Pfizer, the establishment of HELM as an industry standard provided even greater value by facilitating cross-company interoperability and biomolecular data exchange, a very desirable outcome in our increasingly collaborative industry”

Roche:

Starting with HELM Roche has developed the HELM Antibody Editor (HAbE) to enable especially the convenient handling of complex antibody in innovative formats for their analysis, visualization, manipulation and registration.

Most recent is the implementation of HELM2 at Roche to describe, register and manage therapeutic oligonucleotides and their derivates. This was facilitated by the improved monomer handling and support for ambiguous nucleotides within the HELM 2 toolkit.

Merck:

Merck has been slowly adopting the HELM notation across our Discovery Chemistry Modalities organization focusing first on simple linear peptides and oligonucleotides. Using the Pistoia HELM editor for creation, editing and registration of monomers and chemical modifiers, our Modalities chemists can now work confidently with their monomers across multiple environments including our biopolymer registration system, our BioviaDraw platform and our tools within Insight for Excel. In 2018 we anticipate incorporating complex, macrocyclic biopolymers into the HELM supported workflows, peptide metabolite identification support and antibody-peptide conjugates. All of this facilitated by the easy to use tools leveraging HELM notation as a foundation.

Ionis:

Internal registration systems and tools are all based on HELM.

We are grateful to all funders, including the above plus GSK and BMS.

Scientific software providers

Biovia:

Applications use Biovia’s proprietary SCSR (Self-Contained Sequence representation, an extension of the V3000 molfile) format, but there is extensive ability to import, export and convert to and from HELM. Pipeline Pilot Chemistry Collection contains importers and exporters, HELM readers and writers including XHELM, and components to interconvert between macromolecules represented by HELM, full chemistry and SCSR. HELM support is available in Insight, the Draw and Pipette sketchers, biological registration and the chemistry cartridge.

ChemAxon:

Biomolecule Toolkit and the macromolecule sketcher BioEddie are natively supporting the HELM standard. The tools provide capabilities for managing a centralized monomer library, registering and performing uniqueness checks of macromolecules, generating a HELM notation from small molecule representations and sequences, and representing modalities with partially or fully unknown chemical structures.

Roland Knispel, Project Lead for Biologics Informatics at ChemAxon, said, “Our HELM-based tools are helping our customers to manage chemically modified sequence-based modalities. A single environment for various types of modalities, improved data quality and utilizing an industry-wide standard for data exchange are the key benefits reported back to us by our users. By market demand our platform is now being integrated into solutions provided by IDBS and other partners.”

Dotmatics:

Dotmatics has adopted the Pistoia Alliance’s HELM notation as part of its biologics discovery suite. Dotmatics Bioregister reads and writes sequence entities in HELM format, allowing users to work with these entities within the Dotmatics Suite and also to exchange HELM-format data with other HELM-compliant systems. Additionally, we are currently implementing support for HELM in Dotmatics’ analysis and visualization application, Vortex, allowing advanced analytical techniques to be applied directly to HELM-represented entities. These capabilities are available to current Vortex customers in the daily stable builds accessible from the Dotmatics Support website.

IDBS:

IDBS leverages ChemAxon’s Biomolecule Toolkit and BioEddie in its E-WorkBook suite and therefore includes HELM support.

Paul Gouldson, Vice President Strategic Solutions said, “IDBS has been supporting open standards in EWB since its inception. We use and develop integrations to open source tools and have supported examples with AniML, HELM, ADF, SVG and HTML tools.”

Next Move software:

The HELM format is supported by Sugar&Splice both for reading and writing peptides and nucleic acids, thus enabling conversion of all-atom structures from SMILES (for example) through HELM and back to SMILES. This support includes inline HELM (allowing structural data to be roundtripped even when monomers are missing from the HELM database), xHELM and partial support for HELM 2.0 ambiguity codes. The NCBI uses Sugar&Splice to generate HELM strings for all biopolymer entries in PubChem.

RDKit (open-source)

RDKit includes the ability to convert DNA, RNA and peptides to and from HELM and a large number of other notations including: FASTA, PDBBlock and standard sequence notation.

Perkin-Elmer:

PerkinElmer integrated the Pistoia Alliance HELM standard into ChemDraw®, enabling chemists and biologists to easily describe complex molecular structures, rapidly create biopolymeric structures, and share their information in an industry-standard, publication-ready format. “We look forward to continuing to work with HELM as a standard to better serve the research community by providing modern tools that foster collaboration and enable faster discoveries,” says Pierre Morieux, ChemDraw Global Marketing Manager at PerkinElmer.

Quattro research:

Being involved in the HELM tool development from the early hours, quattro research provides solutions for registration of biomolecules based on HELM notation. With a focus on antibodies and ADCs (antibody-drug-conjugate), we have developed the HELM Antibody Editor (HAbE) together with Roche. The xHELM format for data exchange, the ambiguity support of the HELM2 toolkit and a monomer service are additional Pistoia hosted projects developed and maintained by quattro research, in addition to our internal development and research. Many of these tools are now open source and hosted on GitHub, made available to all who are looking into adopting HELM as a standard

Content providers

ChEMBL

ChEMBL is one of the largest public drug discovery databases, containing information about approved drugs, clinical candidates and lead optimization data, including 1.7 million distinct compounds and more than 11,000 targets.

“A large proportion of new drugs are now biotherapeutics, but many could not be adequately represented by our traditional sequence or structure formats. HELM gives us a great solution, allowing us to accurately describe drugs such as modified peptides and antibodies” says Anna Gaulton, Senior Data Integration Officer for the EMBL-EBI Chemogenomics Team.

The ChEMBL database team have worked with the HELM project on methods to fragment peptide structures and define new monomers. These have been used to converted more than 20,000 natural and modified peptide structures to HELM and create a publicly-available library of more than 2800 peptide monomers.

PubChem

PubChem is an open chemistry database at the National Institutes of Health (NIH), which provides information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others to several million scientists worldwide.

Pubchem contains over 500,000 structures represented in the HELM notation. Many of these are complex, for example, only 65% of the HELM peptides are exclusively made up of amino acids.

Report from Pistoia Alliance CDx / NGS & Regulation workshop

Posted on 19 April 2018 by David Prior

Royal Society of Chemistry, London – 11^th April 2018

45 delegates from 30 companies explored the dramatic increase in capability of NGS and its application to CDx. To lead the discussions 5 experts from 5 different domains had been assembled viz: pharma, sequencing quality assessment, notified bodies, regulatory agencies and CDX manufacturers and suppliers.

Here are the key points from the productive day:

Pharma: getting a drug to market was difficult – say just a 3% chance – but understanding the underlying genomics made success twice as likely. As such, NGS and CDx were important.
Quality: by sending test samples to testing labs, the performance of the testing labs could be assessed. Notified bodies were very interested in these performance tests and took them into account when considering quality assessments for CE marking.
Notified Bodies need to become designated by an EU Competent Authority to perform CDx assessments. None have as yet been so designated. Most CDx would fall under EU 2017-746 IVDR Annex VIII Rule 3 and would be determined as class C devices and consequently require Notified Body certification. Once certified, there is an ongoing requirement for CDx performance monitoring and reporting.
Regulatory Agency: the new EU IVDR has imposed significant emphasis on proving the scientific and technical integrity of CDx. By 2022 when the IVDR is put into full application, all existing CDx, and all new CDx , will need to be CE marked under the new regulations. This would put a significant onus onto the Notified Bodies.
The CDx Development and Services providers needed to have in place a robust, standards-based quality management system. Key CDx activities could be broken down into Design Controls, Assay Development, Assay Software, Reagent and Control Manufacture and Regulatory Interaction. NGS assays needed to be validated – but as yet, there was no consensus-based standard way for doing that.

The meeting came to a close after several discussion groups had identified the need for enhanced education and training in the:

rapidly changing NGS technologies,
new developments in bioinformatics (such as containerized software solutions),
roles of quality assessment, regulators and notified bodies in helping users to implement these technologies for precision medicine.

Furthermore, a need was identified to:

Define standards for data, reference genomes, reference materials and QMS,
define some standards for data formats (eg, VCF for regulated applications),
define ways to standardize tools (eg, BWA, GATK), pipelines and processes (eg, containerized tools or workflows) for regulatory applications,
identify commonalities and differences between research and clinical data analysis standards, with the goal of aligning them as much as possible, and
discuss how changes to these processes may impact ethical issues, such as changes to consent and/or data sharing.

The workshop closed with a short networking reception and a common commitment to purse these ideas.

Further information about the project and the speaker’s presentations can be found at https://ip3.pistoiaalliance.org/subdomain/main/end/node/1852

Hack the Lab: SiLA, Deep Learning, Alexa and the CSL

Posted on 16 April 2018 by David Prior

Energy, Collaboration, Lab Data (and Alexa)

For our 2018 European conference we ran our second President’s Series hackathon to show how intensive collaboration can develop new solutions to industry problems.

In under 2 days the teams delivered prototypes and learnings in the areas of the Internet of (Laboratory) Things & AI, developing efficient ways of bringing smart technologies (and not so smart) equipment into the laboratory and demonstrating novel ways to use Pistoia Alliance’s own Chemical Safety Library data to improve laboratory safety.

Here’s a snapshot of the event:

In just a day and a half 7 teams tackled challenges based on our strategic themes of interest and from our project portfolio. We set three challenges:

Predicting Lab instrument failure from Internet of (Laboratory) Things
Integrate smart technology into laboratory process
Improve lab safety with Pistoia Alliance’s Chemical Safety Library dataset

Congratulations to team “Let it go” for winning the hackathon, with their work on the Shire and Tetrascience IOT laboratory instrument sensor data. They impressed their judges with their insight and feedback on the challenges faced if we are to be successful in bringing the Internet of Things into the scientific laboratory. The team were:

Beeta Balalimood, Mood Biopharma Consulting
Daniel Brock, GSK
Alex Brown, GSK
Andrew Conkie, Red Star Consulting

Achievements and learnings:

What did they achieve at the event and what happens next:

Challenge 1: Machine Learning – Predicting lab instrument failure:

Using the Tetrascience and Shire lab instrument sensor data, the teams performed early baselining efforts to understand the normal data patterns of the refrigerators and freezers with the aim of using that to identify any outages. Their initial work, given the limited time, did not deliver a new model but their early insights made it clear that for long term success any sensor infrastructure will need to understand, capture and provide context, namely:

Context / domain understanding of the systems (the users input)
Contextual sensor data: for example not just the temperature and power data from a freezer but a door sensor to know when the freezer / fridge door is open or closed
Contextual usage information: time related information, when was there a service of the instrument or event

Challenge 2: Integrating smart tech and instruments into the laboratory:

Two teams took on the challenge of integrating laboratory equipment, the first used the SiLA libraries to integrate a simple lab process from barcode scanner to multidrop liquid dispenser to analyse and receive LC results. The simplicity of the SilA interface allowed all these pieces of kit to be integrated into a workflow in less than 7 hours of work!

The other team built a demo of a voice activated, hands free laboratory notebook using Google chrome’s voice recognition software. They built a nice demo of controlling and recording the data from a laboratory balance purely by voice control showing with the right skillsets in your team, new innovative solutions with established off the shelf tech can move laboratory processes forward.

Challenge 3: Chemical Safety Library (CSL) Use Cases

Teams had access to our very own Chemical Safety Library data alongside datasets from Merck’s Material Safety Data Sheets and Pubchem. They integrated these with the Amazon Echo speaker and the IOT AWS smart button. We had prototypes for:

Asking about hazard data for a particular compound or reaction
Recording safety incidents:
Immediate logging of incident severity via Amazon smart button
Voice logging of a safety incident through Amazon Alexa
New incident reporting form to link to one of the recorded incident logs

This was all in the space of a day and a half. Here’s a quick video of one of the Amazon Alexa prototypes:

What happens next? Collaboration!

In terms of the hackers:

Already one of our member companies has reached out to Shire and Tetrascience to see if there’s further collaboration on their datasets that can be done.

The University of Southampton team intend to further develop their Chemical Safety Library ideas with Alexa and more. Pistoia Alliance’s Chemical Safety Library team will visit them in the near future to follow their progress. We will keep you posted on this.

As for Pistoia Alliance, the next steps for us are the strategic Communities of Interest in AI and the Lab of the Future, you can find out more about and join them as they move from the discussion phase through to identifying the next Pistoia Alliance collaborative projects for the benefit of the industry.

Join the Lab of the Future Community of Interest
Join the Artificial Intelligence Community of Interest

Thank you to our supporters!

None of this would have been possible without our supporting partners:

For supplying access to Pipeline Pilot and mentorship to the hackers, find out more about their products here.

For supplying glassware and labcoats to get the hackers in the laboratory mood! For providing access to the material Safety data sheets around the Chemical Safety Library challenge, find our more about Merck’s products here

For bringing the lab equipment for the challenge and supporting the hackers as they developed their protoypes. Find out more about SiLA here.

For providing the laboratory sensor data for the Predicting Lab Instrument failure sensor data.

For access to their data and helping bring the CSL data into PubChem. Find out more here about PubChem

For supplying glassware and labcoats to get the hackers in the laboratory mood! Find our more about VWR’s products here

If you’d liek to know more about this hackathon or discuss ideas for future innovation focused events, please contact David Proudlock or one of the Pistoia Alliance team

The Pistoia Alliance Calls for Greater Life Sciences Collaboration to Build the ‘Lab of the Future’

Posted on 19 March 2018 by David Prior

EU conference and two-day ‘hack the lab’ hackathon discusses how artificial intelligence (AI) and the Internet of Things (IoT) will impact life sciences

London, 19^th March, 2018 – The Pistoia Alliance, a global, not for profit alliance that works to lower barriers to innovation in life sciences R&D, is calling upon the industry to support the ‘Lab of the Future’ (LoTF) through greater collaboration. At The Pistoia Alliance’s annual EU member conference in London, president of the Pistoia Alliance, Dr Steve Arlington, urged stakeholders to come together to help technology continue to drive change in the industry and to amplify R&D budgets. Other speakers, including from Merck, GlaxoSmithKline, and SAP, also discussed how future technologies like AI and the use of Real World Data (RWD) will contribute to the development of the lab. Throughout the conference, the goal was to identify key areas where The Pistoia Alliance can set up collaborative projects that will make a real difference to research and ultimately to patients.

“For the past 20 years the lab has looked largely the same. But in that time, how scientists and researchers work and live has changed dramatically. If pharmaceutical companies want to support R&D outcomes that truly benefit patients, then building the Lab of the Future is paramount,” commented Dr Steve Arlington, President, The Pistoia Alliance. “R&D budgets in the life sciences are under greater strain than ever before. Couple this with increasingly stringent regulatory issues and the shifting political situation around Brexit – and pharmaceutical companies are under pressure to deliver. They must now seek ways to amplify their budgets through greater collaboration, cooperation, and data sharing, and by exploring future technologies that will change the lives of patients.”

A second, guest keynote was given by William (Bill) Burns, former CEO of Roche Pharmaceuticals and now a member of The Pistoia Alliance’s Advisory Board. Bill spoke to Alliance members on the current models of pharmaceutical R&D and the commercial challenges the industry faces. Bill discussed how society’s desire for new medicines and healthcare intervention has grown, but that there is a funding gap in how innovations are delivered. He also discussed the need for pharmaceutical companies to accurately measure the medical benefit of a therapy for a patient, so that society and payers reward a drug with a price that enables a return on the investment and risk taken by the shareholders. To enable this, Burns noted, innovation happens at the interfaces, not in the silos – and greater collaboration is required.

As part of the conference, a key agenda item was an update on The Pistoia Alliance’s President’s Series Hackathon held on the 12^th and 13^th of March. The theme was ‘Hack the Lab’ and the event brought together stakeholders from life sciences, healthcare, academia, and technology. The hackathon entailed a series of challenges, focused on AI insight, the ‘Future Corner’, and health and safety for the LoTF. Participants aimed to build prototypes to show how to use AI to interpret instrument logs, explore how new tools can transform the lab, and to find novel uses for datasets and associated lab data. Participants experimented with Amazon Alexa, Google Home, and Microsoft Cortana, as well as AR interfaces, VR headsets, and ‘smart’ glasses. Among the winners were a team from The University of Southampton, who created a ‘friendly’ lab safety assistant based on Alexa, using data from The Pistoia Alliance’s Chemical Safety Library.

The Pistoia Alliance’s European conference was attended by 165 life science professionals from top 10 pharma companies, leading biotechs, and tech firms. Speakers and panel attendees converged on a range of topics – including a panel on how data security can be an enabler in life science innovation, moderated by Richard Horne of PwC. A presentation on why collaboration is essential to the development of new medicines was delivered by Dr Menelas N Pangalos of AstraZeneca. The Pistoia Alliance was created to address the barriers and challenges that companies face during life sciences R&D. Recent successful projects include the Chemical Safety Library Service (CSL), the AbVance Project, and the launch of the User Experience for Life Science (UXLS) Toolkit. In 2017, the Alliance also surveyed members views of blockchain and AI in life sciences, to identify where the Alliance can help support adoption.

For more information about The Pistoia Alliance, please visit: pistoiaalliance.org.

–ENDS–

About The Pistoia Alliance:

The Pistoia Alliance is a global, not-for-profit members’ organisation made up of life science companies, technology and service providers, publishers, and academic groups working to lower barriers to innovation in life science and healthcare R&D. It was conceived in 2007 and incorporated in 2009 by representatives of AstraZeneca, GSK, Novartis and Pfizer who met at a conference in Pistoia, Italy. Its projects transform R&D through pre-competitive collaboration. It overcomes common R&D obstacles by identifying the root causes, developing standards and best practices, sharing pre-competitive data and knowledge, and implementing technology pilots. There are currently over 80 member companies; members collaborate on projects that generate significant value for the worldwide life sciences R&D community, using the Pistoia Alliance’s proven framework for open innovation.

Media Contacts:

Carmen Nitsche

Pistoia Alliance

+001 510-589-3355

carmen.nitsche@pistoiaalliance.org

Michelle Allison

Spark Communications

+44 207 436 0420

michelle.allison@sparkcomms.co.uk

Major new release of the HELM antibody editor (HAbE2) adds support for automated reactions, ADC designer, monomer designer and more.

Posted on 22 February 2018 by David Prior

The release of the HELM Editor by the Pistoia Alliance in 2013 inspired a team at Roche and quattro research to use this technology for the registration of antibodies engineered at Roche’s research sites. The first version was released to the open source community in 2015, but work continued, and a comprehensive set of enhancements has been included in this new release.

In former years, antibodies have followed nature’s standard format: A set of 2 identical light and heavy chains forms an antibody. In current research projects increasingly complex formats are designed by the scientists. These formats pose a challenge to fully describe their chemical structure.

While the HELM Editor provides the power to efficiently build and describe all kind of biologicals, its canvas doesn’t really scale with large molecules like antibodies. Especially if novel antibodies do not follow nature’s standard and the localization of the Cys-Cys bonds within and between domains and chains isn’t straightforward.

To tackle this challenge, the team led by Stefan Klostermann (Roche Innovation Center Munich) developed the HELM Antibody Editor (HAbE). Like the HELM Editor, that is essentially based on a monomer library, HAbE employs a domain library to describe the functional building blocks of antibodies and other conjugated proteins. Based on this library, HAbE decomposes raw protein sequences of even complex antibody formats into their domains and fully analyzes and annotates them. This process is supported by a mutation library that enables the identification of known mutations in standard domains.

Using an integrated auto-connector algorithm, HAbE also aims to automatically assemble the complete drug molecule into its complete final structure by finding the correct Cys-Cys bonds. The underlying rules are laid down in a flexible, user customizable syntax describing advanced formats and functional modules like scFV/ scFab. The GUI enables further editing of the molecule to close Cys-Cys bonds not yet covered by the rule set.

The HAbE2 release adds major new functionality to multiple enhancements under the surface. Now, automated reactions can be carried out, including: Domain Protease Reactions, Sortase Coupling and Biotinylation. There is also an Antibody Drug Conjugate Designer which allows the scientist to define statistical binding ratios defined for the attachment of chemical molecules to the antibody and a Monomer Designer, so new monomers can be designed, used and stored.

These enhancements to one of the most sophisticated applications in the HELM family further cements HELM as the industry standard for the description of biological macromolecules.

More information can be found in our wiki and the HELM team can be contacted at info@openHELM.org.

Use of Next-Generation Sequencing in the regulated domain of drug development

Posted on 13 February 2018 by David Prior

in the article “Use of Next-Generation Sequencing in the regulated domain of drug development“, Pistoia Alliance’s Keith Nangle and Mike Furness discuss how Next-Generation Sequencing is moving quickly from early research into the regulated domains of drug development, diagnostic development, and clinical decision-making.

This article summarises some of the technical and regulatory challenges posed by these technologies and the efforts being made to address them.

Reproduced with kind permission from Drug Discovery World Winter 2017/18 Volume 19 Number 1.’

Download from the box below or click here.

The Pistoia Alliance Tackles Poorly Designed Scientific Software with Launch of User Experience for Life Sciences Toolkit

Posted on 13 February 2018 by David Prior

Global collaborative project delivers toolkit to promote best practice and accelerate productivity; conference to be held in May 2018 will showcase importance of user experience design

London, February 13, 2018: The Pistoia Alliance, a global, not-for-profit alliance that works to lower barriers to innovation in life sciences R&D has today announced the launch of the User Experience (UX) for Life Sciences (LS) Toolkit, to help life science companies improve UX in line with other global industries. The UXLS toolkit marks the culmination of a collaborative project involving more than 50 UX specialists from 20 different organisations across the world; including several top ten pharmaceutical companies, bioscience, and technology firms. The toolkit contains UX case studies, methods, and metrics – enabling life science companies to design better, more intuitive, more usable digital products, specifically for R&D in the life science and healthcare environment. These issues and the benefits of UXLS for improving productivity will be discussed further at The Pistoia Alliance’s User Experience for Life Science conference on the 14-15^th May 2018 in Boston, USA, featuring keynote speakers from companies including Novartis.

“In today’s world, software is the gateway to unlocking the many zettabytes of data that humans produce. When scientific software is poorly designed, it is frustrating and time-consuming to use, and adds yet another barrier to the acceptance and adoption of new digital technologies, such as automation and Artificial Intelligence. This has the cumulative effect of making drug discovery and development far less efficient and productive,” commented Dr Steve Arlington, President of The Pistoia Alliance. “As we become more familiar in our personal lives with digital technologies that interact intuitively and respond to our needs, the desire for technology that ‘just works’ in our professional lives is also growing. The potential for good UX design to impact life science R&D is significant – from improving the UX of clinical trials and making it easier for patients to participate, to delivering cutting-edge UX design that supports the ‘laboratory of the future’. UX design should not be considered a remote or niche area, and we hope that our UXLS toolkit enables more companies to realise this potential.”

The UXLS project was formed by The Pistoia Alliance in recognition of the fact that many life science organisations are behind the curve when it comes to UX. Although UX principles are widely recognised and have been applied successfully in other industries, such as retail and financial services, adoption and use in life science is low. Members of The Pistoia Alliance communicated this issue, and the UXLS project began as a result in early 2017. The project empowers life science professionals to realise the benefits that UX design can deliver through engagement with a wider audience, including stakeholders in senior management. The global UXLS project team worked collaboratively to develop the toolkit which provides a ‘how-to’ that helps businesses adopt UX principles and methods as they develop scientific software.

“At EMBL-EBI, we have a mandate to share data from life science experiments, and put a lot of energy into helping people make the best possible use of it,” says Professor Ewan Birney, Director of the European Bioinformatics Institute. “We experienced a big change when we re-focussed the development of our services and started to adopt a user-centred design process. We benefited from doing user research, prototyping, design and testing to get to the heart of the problem and deliver products and services that are intuitive for researchers. I was initially sceptical, but then I was impressed to see the results across our organisation.”

The UXLS toolkit so far contains six case studies from organisations such as Novartis, EMBL-EBI, and AstraZeneca; 10 published methods, such as interactive prototyping and usability testing; meaningful principles that will assist and explain activities to better a system or process. The toolkit will be beneficial for UX practitioners, bioinformaticians, software developers, and technical and IT managers. The UXLS conference will be hosted by Novartis at the Novartis Institutes for BioMedical Research (NIBR). Pat Keller, Global Head of User Experience at NIBR will deliver a keynote speech at the conference, which will also feature several ‘hands on’ UX workshops.

For more information on the UXLS project and toolkit, please visit: http://www.pistoiaalliance.org/projects/uxls/ and http://uxls.org.

For more information on the UXLS conference, please visit: http://www.pistoiaalliance.org/eventdetails/user-experience-life-science-conference/.

— ENDS –

About The Pistoia Alliance

About the European Bioinformatics Institute (EMBL-EBI)

The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind. We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease. We are part of EMBL and are located on the Wellcome Genome Campus, one of the world’s largest concentrations of scientific and technical expertise in genomics. Website: www.ebi.ac.uk

Pistoia Alliance President’s Series Hackathon – Hack the Lab, Registrations Open

Posted on 26 January 2018 by David Prior

Hack the Lab!

The Pistoia Alliance is bringing together the life-science, healthcare and technology industries to collaborate and advance the scientific laboratory.

We invite you to come and HACK THE SCIENTIFIC LABORATORY! Help us build the future, smarter, more efficient and safer lab!

This year’s challenges will focus on:

An exciting 2 day event to develop ideas into prototypes, win prizes and more!

Let’s collaborate to bring new ideas and technology to advance how the Lab of the Future will run.

In return you can:

Win Prizes
- Overall winning team: £1500
- Individual challenge winning team’s: £750)
Enhance your personal development and career
Network
Have fun!

Come and join Pistoia Alliance’s Hack the Lab!

Interested in attending?

Find out more and register here

Can’t attend but interested in supporting the event?

There are options to either support one of our challenges or sponsor the event.

Support:

Do you have datasets, equipment or an idea for a challenge?

Sponsor:

Opportunities to sponsor this year’s event are also available.

Contact David Proudlock or one of the Pistoia Alliance team for more information

44% of Life Science Professionals Already Using or Experimenting with AI and Deep Learning, Finds Survey from The Pistoia Alliance

Posted on 9 January 2018 by David Prior

94% expect an increase in use of Machine Learning within two years, but access to quality data and technical expertise is a barrier to adoption

Boston, January 9th, 2018: The Pistoia Alliance, a global, not for profit alliance that works to lower barriers to innovation in life sciences R&D, is calling on the pharmaceutical and technology industries to support greater collaboration around Artificial Intelligence (AI) in pharmaceutical R&D. The Pistoia Alliance surveyed the views of 374 life science professionals on AI, Machine Learning (ML) and Natural- Language Processing (NLP). The survey found interest in these technologies is high, with almost half (44%) of respondents already using or experimenting with AI. However, a number of hurdles to their widespread application were also identified – with technical expertise the most cited barrier for AI (30%) and for ML/NLP (28%). The Pistoia Alliance believes collaboration between stakeholders is essential to overcoming these barriers; leading to ‘augmented’ AI that works alongside humans for positive outcomes. In particular, given how crucial data is to building AI algorithms that reveal meaningful insights, collaboration over data standards, benchmark sets, and data access, will be essential.

The survey found that beyond a lack of in-house technical expertise, issues around data are a particular stumbling block to AI projects. Specifically, respondents stated that access to data (24%) and data quality (26%) were two of the biggest barriers to AI projects within their organisation. These same issues – access to data (26%) and data quality (19%) – were again cited when respondents were also asked about obstacles to ML and NLP projects. Life sciences and pharmaceutical R&D currently generates huge volumes of data, which is supplemented with growing data sets collected from mhealth devices and sensors connected to the Internet of Things (IoT). However, access to this data and the formats that data are stored in, vary wildly. Quality data is fundamental in ensuring AI gives accurate and true outputs; this is a significant finding, and one the industry will need to overcome in order for AI to assist researchers.

“AI has the potential to revolutionise life sciences and healthcare – all the way from early preclinical drug discovery to selecting precision treatments for individual patients,” commented Dr Steve Arlington, President of The Pistoia Alliance. “Our survey data shows that while life science professionals are already exploring how AI, ML and NLP can be used – there are clear gaps in the knowledge, data, and skills, which will enable more pharma and biotech companies to achieve tangible results from AI. Impediments to success, such as a lack of industry-wide standards for data format, will need to be addressed, if the potential of AI and ML is to be realised. We urge those in the pharmaceutical, biotechnology and technology industries to explore ways in which they can collaborate now, to find answers to common problems of the future.”

When asked about the use of AI and associated technologies, the results revealed applications are varied. The majority (46%) of AI projects currently take place in early discovery or preclinical research phases; NLP is also employed by just under a third (30%) during early phase research. Other applications of AI were given as development and clinical (15%), and imaging analysis (8%). More than a fifth (23%) of respondents are using ML for target prediction and repositioning, followed by biomarker discovery (13%) and patient stratification (5%). However, adoption is not universal; a notable number of respondents are not using AI (11%), NLP (27%), or ML (30%), at all. Moreover, 8% of respondents admitted they knew ‘next to nothing’ about AI and Deep Learning, highlighting the need for greater education and knowledge sharing

“It is clear that while some early-adopting companies are already employing AI, ML and NLP, there are others that have not yet explored these technologies,” commented Dr Nick Lynch, consultant for The Pistoia Alliance. “While the adoption of AI and associated technologies is in its nascent stages, we firmly believe that for all patients to eventually benefit, a pooling of knowledge is vital. Collaboration will be key to finding the areas, for instance, where AI is good enough to augment and work in parallel with humans. To provide such a forum for knowledge sharing, The Pistoia Alliance has launched an AI and Deep Learning community – bringing together interested parties to share their expertise, as the industry continues in its quest for new medicines that make patients’ lives better.”

The Pistoia Alliance’s AI and Deep Learning community will be focusing on two main areas. Firstly, supporting awareness and adoption of AI though sharing best practice, and secondly, developing and sharing best practice about data – for more information, see here. Two surveys of 374 senior pharmaceutical and life science leaders were conducted via webinar in September 2017. For information and slides from the webinars, see here and here.