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Author: David Prior

HELM editor: free at last!

Posted on by David Prior

The Pistoia Alliance HELM project announces free MarvinBeans 5.0 licenses and integration of HELM with the RDKit cheminformatics suite

Wilmington, DE – The Pistoia Alliance HELM project has made two major announcements that help cement the reputation of HELM as the de-facto standard for describing and working with complex macromolecular structures. Firstly, HELM users can now take advantage of free MarvinBeans 5.0 licenses for the HELM toolkit. Secondly, RDKit is now HELM-enabled, making it a valuable addition to the extensive range of open source HELM-enabled tools.

As a very strong supporter of the HELM standard (Hierarchical Editing Language for Macromolecules), ChemAxon has agreed to issue a free license for the utilization of the MarvinBeans v5.0 library within the HELM toolkit, thus negating the previous requirement for end-users to purchase a license. This removes a major barrier to fully free utilization of HELM by potential adopters, and is a very generous gesture that further highlights ChemAxon’s belief in the power and value of the HELM standard.

“This is a significant development for the HELM project,” said Sergio Rotstein, Director of Research Business Technology at Pfizer and Domain Lead for the Pistoia Alliance HELM project. “Thanks to the generosity and vision displayed by ChemAxon, HELM can now be distributed and utilized at no cost to adopters, which further aligns with the true spirit of Open Source. We are grateful to ChemAxon for their commitment to pre-competitive collaboration, and are confident that this will have a positive impact on continued adoption of HELM across our industry.”

ChemAxon’s Jon Patterson said “We are pleased to take part in this milestone for the HELM project and the role it will play with increased adoption of the standard. We look forward to continued collaboration with the Pistoia Alliance as the initiative evolves.”

In addition, the HELM project is pleased to announce the implementation of HELM import and export capabilities in the RDKit chemical toolkit. This functionality, developed independently by NextMove Software, provides an important bridge between chemical and biomolecular space, particularly for computational scientists that want to utilize RDKit’s deep cheminformatics capabilities in the context of larger entities such as peptides and proteins. It also provides organizations with a tool that can enable the conversion of their existing collections of macromolecules into HELM.

Sergio Rotstein commented, “The new functionality in RDKit is an exciting indicator of good health for the overall HELM project, with a steadily-growing list of individuals and organizations outside of the core project team contributing new functionality to the codebase and integration with other technologies.”

Author Roger Sayle of NextMove Software added, “As a contributor of both Java code to the Pistoia Alliance’s HELM toolkit and C++ code to RDKit, bridging these two communities by adding HELM peptide support to RDKit seemed like a logical next step.”

Greg Landrum, Global Head of Chemical Information Systems at the Novartis Institutes for BioMedical Research and lead of the RDKit open-source project added: “As we start to use HELM in our systems for registering sequence-based biologics within NIBR, it’s fantastic to be able to use the same open-source tooling that we apply to small molecules. I’m looking forward to an ongoing collaboration with NextMove Software and the rest of the HELM community to expand on RDKit’s ability to handle HELM.”

The HELM standard has attained a tremendous growth in popularity in the R&D informatics space since its initial release in 2012. Before HELM there were no tools available for scientists to rigorously represent complex biomolecules (e.g. bioconjugates, unnatural peptides) in their systems, leading to “pick and mix” approach of multiple nomenclatures and textual descriptions. HELM provides a one-stop-shop solution consisting of an open standard and accompanying toolkit that enables the representation of a wide range of biomolecular entities including oligonucleotides, peptides, proteins, antibodies and drug-antibody conjugates, supporting both the natural and non-natural building-blocks commonly used today.

About ChemAxon

ChemAxon provides cheminformatics software platforms, applications and services to optimize the value of chemistry information in life science and other R&D. Our mission is to enable scientists to manage their chemical and related data via intuitive, powerful and cost effective informatics tools, developed together with our customers and partners. www.chemaxon.com

About NextMove Software

NextMove Software develops innovative informatics solutions to support the pharmaceutical and chemical industries. Founded in 2011, NextMove Software’s products are used by 8 out of the top 12 pharma companies. In addition, to its commercial operations, NextMove Software’s employees also contribute to several open source cheminformatics projects, including RDKit, HELM, CDK, Open Babel and OPSIN. www.nextmovesoftware.com

Pistoia Alliance Launches New Chemical Safety Library Project

Posted on by David Prior

New project will help improve safety in life science and chemistry research

CSL_logo_rgb_242pxWilmington, DE – The Pistoia Alliance, a not for profit organization working to improve collaboration in the life sciences industry, has started work on the Chemical Safety Library, a project which will allow for the capture and sharing of previously inaccessible reaction incident information to enhance laboratory safety.

The research enterprise inherently will always involve some risk, as novel compounds are created and new combinations are explored. In addition, data on adverse events that took place in the past or in another organization are difficult to impossible to access when planning new experiments, leading to the potential for repeat occurrences.

The Chemical Safety Library will see the creation of an informatics driven resource to allow all organizations to effectively share chemistry-related incident reports, delivering value from real life incidents and learnings. The data will be collected in a publicly available central resource and rule sets and triggers will be created that can be tied to scientists’ reaction planning tools, so that if an organization should attempt to repeat a procedure that previously resulted in an accident, a warning will be issued.

Through collaboration across the industry and with publishers and suppliers, the Chemical Safety Library will leverage the incident system to define and promote standards to make more traditional hazard information more actionable as well. These outputs will be beneficial as industry and academia strive for continuous improvement in hazard communications.

Dr Steve Arlington, President of the Pistoia Alliance, said: “Chemical safety is something the industry takes very seriously and risks are carefully minimized through regulation and good safety practices, but there is still the risk of unexpected adverse incidents. As the industry relies on experimentation to develop new products, there is no way to eliminate risks entirely, but through the Chemical Safety Library researchers can begin sharing previously inaccessible information on potentially hazardous activities and improve chemical safety for all.”

The launch of the Chemical Safety Library builds on the success of the Pistoia Alliance’s other ongoing projects, HELM (Hierarchical Editing Language for Macromolecules) and the CSCS Expert Community (Controlled Substances Compliance Services), both of which have seen widespread adoption of their outputs throughout the life sciences sector. In addition to these successful projects, the Alliance has recently launched the Ontologies Mapping project, and has announced the finalists for the first Pistoia Alliance President’s Start Up Challenge.

ELIXIR and Pistoia Alliance to Collaborate on Map of Alliances

Posted on by David Prior

ELIXIR_logo_white_backgroundHinxton, UK – ELIXIR and the Pistoia Alliance will be collaborating as part of the Map of Alliances project, an industry initiative to better understand the landscape of the pre-competitive environment in life sciences.

The collaboration will see ELIXIR and the Pistoia Alliance map out the landscape of life science organisations, including industry, academia and not for profit, and identify their interconnections, overlaps, similarities and differences.

Describing this complex network will help ELIXIR understand how they fit and feed into ELIXIR community and industry outreach, training strategy, and the ELIXIR capacity building programme. Under the banner of its Map of Alliances project, the Pistoia Alliance will use the data to better understand where it sits within the competitive landscape of pre-competitive collaborations.

The Pistoia Alliance is a global, non-profit consortium of companies, vendors and publishers that work together to lower barriers to innovation in the life sciences industry. The Pistoia Alliance will bring to this collaboration the necessary industry perspective, and connect the project to their members and industry partners. Both the Pistoia Alliance and ELIXIR will also invite other organisations to participate in the project.

All data gathered and systems developed during the course of the project will be freely available for reuse by the public and other researchers. By sharing this data it is hoped that everyone may better understand the nature of life science collaborations and the range of options on offer to organisations considering starting a collaboration of their own.

Community workshop, 19 November 2015, Hinxton, UK

ELIXIR and the Pistoia Alliance already started working on the common specifications to describe life science organisation as part of the Specificaton Hackathon, which happened on 20-21 October in Birmingham, UK. The event brought together experts from ELIXIR, Pistoia Alliance, GOBLET and BioSharing to work on common standards in discovering and collecting information about life science organisations, events and training materials. The formal launch of the collaboration will take place at a joint workshop on 19 November 2015 in Hinxton, UK as a satellite meeting of the BioMedBridges symposium. Register via email at: community@bioschemas.org.

Pistoia Alliance partners with quattro research GmbH to implement “Ambiguous HELM”

Posted on by David Prior

Munich, October 14th, 2015 – The Pistoia Alliance, a global alliance of life science companies, vendors, publishers, and academic groups, has selected quattro research GmbH to implement the HELM 2.0 project (“Ambiguous HELM”). This initiative will enable HELM to represent biomolecules in which some aspects of the structural composition or assembly are not fully determined.

Scientists have struggled to represent non-standard biomolecules in their systems leading to “pick and mix” approach of multiple nomenclatures and textual descriptions. HELM, the open standard, enables the representation of multiple types of complex macromolecules including nucleotides, proteins, antibodies and drug-antibody conjugates including ones containing non-natural elements.

Created by a team at Pfizer, the Pistoia Alliance formalized the HELM notation as an open standard in early 2013 and publicly released software tools to the Open Source community. Since its release, HELM has benefited from a growing range of global adopters and contributors, which includes ACD Labs, Arxspan, Biomax, Biovia, BMS, ChemAxon, EMBL-EBI, eMolecules, GSK, Lundbeck, Merck, NextMove, Novartis, Pfizer, quattro research, Roche, and Scilligence.

While the existing HELM approach solves the problem of representing unnatural complex biomolecules, it still assumes that the scientist knows everything about the structure. In biology this is rarely the case, with the outcome of experiments subject to a number of uncertainties. Currently scientists have a difficult choice: either imply they have all the information and guess at a structure, or record a textual description and put no structural information in their corporate databases. Ambiguous HELM allows the structural information that is available to be captured in a useful way, while also identifying what is not known.

The HELM 2.0 project aims to implement a number of enhancements to the current HELM definition and open source codebase:

  1. Extend the HELM notation and the HELM toolkit to allow for the representation of ambiguous macromolecules.
  2. Create an API which allows the toolkit to access different chemical libraries.
  3. Create web-services for the toolkit to abstract the toolkit functionality from the code implementation.

“HELM has already delivered a practical way for researchers to represent complex biomolecules computationally. Through our partnership with quattro research, HELM will now be able to gracefully deal with the all-too-common situation of entities with uncertain or ambiguous structural features, an important expansion in the usability – and consequently – the adoptability of the technology” said Sergio Rotstein, Director of Research Business Technology at Pfizer and Domain Lead for the Pistoia Alliance HELM initiative, comment.

Markus Weisser, Managing Director at quattro research GmbH added: “HELM is designed as an open source project. Hence, it is important that we now start to remove third party dependencies and provide a more service-oriented architecture. This will lower the barriers to contributing to the development of HELM and attract even more companies to join the HELM community. During the last one and a half years, quattro research has become a leading expert in HELM and its extensions. We have helped to develop the extension xHELM and contributed to the development of the HELM Antibody Editor. We are very proud that the Pistoia Alliance has chosen us to implement HELM 2.0 and look forward to another successful collaboration.”

About the Pistoia Alliance:

The Pistoia Alliance is a global, not-for-profit alliance of life science companies, vendors, publishers, and academic groups that work together to lower barriers to innovation in R&D. Our projects transform R&D innovation through pre-competitive collaboration. We bring together the key constituents to identify the root causes that lead to R&D inefficiencies. We develop best practices and technology pilots to overcome common obstacles. Our members collaborate as equals on open projects that generate significant value for the worldwide life sciences community. www.pistoiaalliance.org.

About quattro research GmbH:

quattro research GmbH is a software and service company located in Munich, Germany. quattro research offers services and products for data management in the pharmaceutical, chemical, and biotech industry. The primary focus of the company is the development of tools and services for compound registration and analysis of biological data. Within several projects, quattro research developed extensive knowledge in the management and registration of biologics, e.g. antibodies and peptides. For further information see www.quattro-research.com or email weisser@quattro-research.com.

Finalists Announced for Pistoia Alliance President’s Startup Challenge 2015

Posted on by David Prior

Newly launched business plan contest has attracted cutting edge companies from around the world.

startup-242Wilmington, DE, 13th October 2015 – The shortlist of finalists for the Pistoia Alliance President’s Startup Challenge 2015 was announced today, showcasing a range of startup companies with exciting new ideas from across Europe and the USA.

The Startup Challenge 2015 has seen startup companies from around the world develop new ideas to lower the barriers to innovation in life sciences R&D, with over 30 entries submitted. A panel of expert judges drawn from the Pistoia Alliance’s membership reviewed all entries and provided detailed written feedback to each one.

The five entries selected as finalists by the judges include:

  • BSSN Software GmbH (Germany): software to improve access to scientific data through an integrated approach
  • Informatics Unlimited (UK): services and novel informatics solutions for Life Science R&D organisations
  • Novaseek Research (USA): a platform that enables access to real-world real-time clinical data and human biospecimens to accelerate R&D
  • Ontoforce (Belgium): pioneering technology for information flow and management
  • Repositive Limited (UK): provision of efficient access to genomic data through a novel platform

The finalists were presented with their awards by Dr. Steve Arlington, President of the Pistoia Alliance, at the Pistoia Alliance US Conference 2015 in Philadelphia. The finalists will each receive three months’ mentorship from a Pistoia Alliance member company and a small cash prize of US$5,000 to help them develop their business plans further.

Final judging will take place in January with the overall winners announced at an awards ceremony in London, UK, in February 2016. The winners will each receive an additional cash prize of US$15,000 and a further six months of expert mentorship. Mentors in the Startup Challenge are senior industry figures drawn from the Pistoia Alliance membership, offering valuable industry insight to the Finalists and Winners and a chance for them to validate their ideas against real industry needs.

Dr Steve Arlington, President of the Pistoia Alliance, said: “We are delighted to have attracted such a range of excellent companies from around the world. Technology will allow us to support cost effective healthcare delivery in exciting new ways in the future. Life science and biotech startup companies like these are already making an impact globally, and with support from the Pistoia Alliance we hope to accelerate the progress and impact of our finalists in this highly competitive market. Small businesses are crucial to the development of new innovations in life sciences and we hope that by supporting these companies we can lower the barriers to innovation globally.”

Jaroslaw Tomczak, Founder and Director of one of the finalists, Informatics Unlimited Ltd., said “We are thrilled to have reached the final of the Startup Challenge and enormously grateful to the Pistoia Alliance for organising this competition. It is a unique opportunity for small businesses like ours to validate novel ideas and to receive critical advice from life science industry experts. In particular, we want to thank the judges who provided us with very valuable feedback and we look forward to working with our mentor on boosting our product vision.”

Pistoia Alliance Appoints Steve Arlington As President

Posted on by David Prior

08_Steve_Arlington_015Wilmington, DE, 13th October 2015 – The Pistoia Alliance has appointed Dr Steve Arlington as its new President. Steve joins as the Pistoia Alliance continues to drive to increase the organization’s impact on the global innovation landscape in life sciences R&D.

The non-profit Pistoia Alliance is focusing its vision and expanding its work in supporting pre-competitive collaboration in the life sciences sector. Steve brings new leadership to an already active organization with a growing number of sector-wide members, collaborations and a remit to continue the transformation of the life sciences industry through innovative new approaches.

Steve previously was the Global Lead Partner, Pharmaceuticals and Life Sciences consulting at PwC where he was responsible for leadership and growth of the global team. He also headed the influential pharma thought leadership series Pharma 2005, Pharma 2010 and Pharma 2020. Steve began his career in research at Smith Kline, and has held senior roles at Unipath, PA Consulting and IBM. He has also led a biotech business and served on a number of supervisory boards.

Commenting on his appointment, Steve, said: “This is a very exciting time to be joining the Pistoia Alliance. The global healthcare and life sciences industries are undergoing huge changes, with regulators, payers, providers and patients all demanding more value. Today, there is a need for a marked departure from the traditional models, and technology and innovative applications of technology across the whole health, pharma and life sciences ecosystem will become more important than ever before.

“The Pistoia Alliance is well placed to be at the forefront of this through its cross–industry network. Having already made an impact through a number of initiatives including HELM and CSCS, I look forward to championing new initiatives to support the life sciences sector globally.”

Michael Braxenthaler, outgoing President of the Pistoia Alliance said: “I am delighted to welcome Steve to the Pistoia Alliance. He has a wealth of experience in the life sciences sector, and this will be key to transforming how the sector operates. I am confident that under Steve’s leadership the Pistoia Alliance will continue to grow and demonstrate industry leadership.”