News

Glencoe Software and The Journal of Cell Biology Pioneer Publishing of Genome-Wide Screens

Seattle, USA, September 6, 2011 –The Journal of Cell Biology (JCB), The Rockefeller University Press and Glencoe Software are pleased to announce their next enhancement to the JCB DataViewer, the world's first system for sharing and archiving published scientific image data. Starting today, data from genome-wide high-content screens (HCS) can be published online, directly associated with papers published in JCB. HCS data are increasingly used to determine the effects of systematic disruption of all genes that govern a specific cell biological process. The approach is valuable because it allows scientists to uncover new and unexpected factors involved in physiology and disease and thus helps identify new targets for drug therapy. While these screens are now widely used, venues for sharing the data generated by them and publishing those data in their entirety are limited. The JCB DataViewer now makes these very large datasets readily available via a standard browser interface and easily mined for information through interactive tools developed for this application.

First released in December 2008, the JCB DataViewer has been under continuous development to support new data types and to provide new functionality for its users. This new version of the JCB DataViewer allows authors to archive and share HCS data and allows the scientific community to interactively browse and, for the first time, download original screen data to their own computers for more detailed analysis. Public distribution of these datasets creates opportunities for further discovery by scientists beyond those that performed the original experiments.

The JCB DataViewer currently contains original image data (multi-dimensional image data taken directly from a microscope imaging platform) associated with 195 manuscripts published in JCB, and the image data submission rate by authors is steadily increasing. Publication of HCS data will substantially increase the size of datasets hosted within the JCB DataViewer, but Glencoe Software, Inc. and JCB welcome and are prepared for the growth of this resource. Liz Williams, Executive Editor of JCB, said, "With the publication of our first four HCS datasets, JCB is very excited to be taking this next step in the development of new publishing tools to promote data sharing and discovery in the field of cell biology." Mike Rossner, Director of The Rockefeller University Press, added, "This update to the JCB DataViewer represents a significant advance in our continuing effort to promote data integrity and data sharing, and to enhance the presentation of image data associated with JCB papers."

The JCB DataViewer is based on open source software built by the Open Microscopy Environment (OME). Founded in 2000, OME builds and releases specifications and software tools for scientific image data and its tools are used throughout the academic and commercial communities. Glencoe Software, Inc. has used OME's resources to build the JCB DataViewer and is a proud member of the OME Consortium.

Jason Swedlow, President of Glencoe Software, Inc., and co-founder of OME, said, "OME and Glencoe Software are excited to be a part of this important development and milestone in scientific publishing. OME's infrastructure has many possible applications, and the whole OME team is proud of the work enabling access and sharing of HCS image data in science."

Glencoe Software, Inc. is a member of the OME Consortium and provides commercial access to and customization of OME resources. With increasing proliferation and complexity of research image datasets and the need for secure sharing, analysis, and visualization, Glencoe Software is well-placed to deliver secure, scalable solutions based on an open-source, community-driven foundation. www.glencoesoftware.com

The JCB DataViewer hosts supplemental image data associated with articles published in The Journal of Cell Biology. JCB is published by The Rockefeller University Press, which also publishes The Journal of Experimental Medicine and The Journal of General Physiology. All editorial decisions on manuscripts submitted to the Press journals are made by active scientists in conjunction with in-house scientific editors. All published content is available for free six months after publication. Authors retain copyright to their publications, and third parties may reuse the content under a Creative Commons license.

Pioneering US/Scottish Alliance for Life Science and Clinical Informatics

Seattle, USA and Dundee Scotland September 1, 2011 – Aridhia Informatics Ltd and Glencoe Software have formed a strategic partnership to create innovative products to aid the development of personalised therapies and deliver improved patient outcomes.

Anticipating an increased focus on stratified medicine in coming years, the two companies will work together to create products for the international healthcare, life and biomedical science markets using real world clinical, genetic and research information.

Aridhia’s specialist capabilities in accessing, storing and analysing health care information will be brought together with Glencoe’s expertise in managing, sharing and publishing large scientific datasets generated in laboratories around the world.

As part of the agreement, Scottish company Aridhia will make a major investment in Seattle-based Glencoe to further accelerate its already-rapid growth in these areas.

Both Glencoe Software and Aridhia Informatics are start-ups based on technology and expertise developed at the University of Dundee, Dundee, Scotland.

Professor Peter Downes, Principal of the University, said: "Dundee is a great place for life sciences companies, such as Aridhia and Glencoe to do business. Their collaboration here will create jobs and further strengthen our innovation economy. It is good news for Dundee and good news for Scotland. "

Professor Andrew Morris, Director of the Medical Research Institute at the University of Dundee, and co-founder of Aridhia Informatics said: “This partnership brings together complementary strengths needed to accelerate the innovation of stratified – or personalised – medicines. Our vision is to become a world leader in providing the clinical and scientific information required for the personalised, targeted drugs and treatments of the future. The UK is a good place to do this work because of the opportunities for open innovation between NHS, academic and commercial partners.”

Professor Jason Swedlow, President of Glencoe Software, Inc., and co-founder of OME, said: "OME and Glencoe Software are particularly excited about this partnership. We look forward to working with the Aridhia Informatics team to develop new tools for the life sciences and clinical data markets. The challenge is huge, but the potential benefit for biomedical research and patient outcomes is enormous."

Aridhia Informatics is a joint venture between the University of Dundee, NHS Tayside and Sumerian. Aridhia provides a unique combination of clinical expertise, academic excellence and high performance computing experience to generate real time information services that improve the safety, quality and efficiency of health care. The company has raised over £6.5M of external capital investment since it’s founding in 2008.

Glencoe Software, incorporated in Seattle, USA has developed technology platforms that are based on open source software built by the Open Microscopy Environment (OME). Founded in 2000, OME builds and releases software tools for the analysis of very large scientific image datasets. Its tools are used globally throughout the academic and commercial communities. Glencoe Software is a major contributor to OME's efforts, and has used OME technology to build many different products, including the Journal of Cell Biology DataViewer , the world's first on-line scientific image data publication system and various solutions for microscopy and high content screening in the academic and pharmaceutical markets.

Dr David Sibbald, Chairman of Aridhia, said: "We relish the opportunity to partner with Glencoe. This will act as an accelerator to link the laboratory to the clinic. We see this investment as prescient with the real prospect of using individual genetic and imaging information to tailor treatment for individual patients, so called personalized medicine. We anticipate it will not only deliver real benefits to patients and health care professionals, but also will deliver economic advantages associated with world leading, unique research.”

About Aridhia Aridhia Informatics is a multidisciplinary health informatics company whose goal is to improve the quality, efficiency and delivery of health services, and make a real impact on patients’ lives through health care analytics. A joint venture between NHS Tayside, the University of Dundee and Sumerian, Aridhia provides a unique combination of clinical expertise, academic excellence and high performance computing experience to generate a unified patient view of healthcare event information, including specific services for patient tracking, clinical dashboards and long term condition management tools. Aridhia is also the lead development partner in the Kuwait Scotland eHealth Innovation Network, which aims to draw upon best practice in Kuwait and Scotland to develop systems for high quality patient care in Kuwait. www.aridhia.com

About the University of Dundee The University of Dundee is internationally recognised for its excellence in life sciences and medical research with particular expertise in cancer, diabetes, cardiovascular disease and skin diseases. The University has a top-rated medical school with research expanding from "the cell to the clinic to the community", while the College of Life Sciences is home to some of the world's most cited scientists and more than 800 research staff from 60 different countries. www.dundee.ac.uk

About Glencoe Software Glencoe Software, Inc. is a member of the OME Consortium and provides commercial access to and customisation of OME resources. Glencoe Software focuses on enterprise level, mission critical scientific image database tools and deployment strategies. With increasing proliferation and complexity of research image datasets and the need for secure sharing, analysis, and visualisation, Glencoe Software is well placed to deliver secure, scalable solutions based on an open-source, community-driven foundation. www.glencoesoftware.com

Glencoe Software and Open Microscopy Environment Founder Awarded the BBSRC Innovator of the Year 2011

Seattle, March 30, 2011 – Glencoe Software Inc. Glencoe Software, a leading provider of image data management tools for life science and biopharmaceutical research and a member of the Open Microscopy Environment Consortium is proud that its founder Professor Jason and the whole OME Team have been named this year’s BBSRC Innovator of the Year. The BBSRC is the United Kingdom’s primary funder of academic research and training in the non-clinical life sciences, and along with the Wellcome Trust, a major funder of research and development undertaken by the OME Team. The Innovator of the Year Award recognizes individual and institutional commitment to realising the social and economic potential of excellent research.

The judges' view was that the impact of OME was of remarkably wide benefit due to the flexibility and openness of the approach. The business model is very clever and allows for open source software development - as in, for example, Linux, Java, Mozilla's Firefox - and at the same time commercial opportunities are possible by licensing and commercialization of Bio-Formats through Glencoe Software. In this way there are both economic and social impacts from the work.

Prof Swedlow founded OME along with Dr Peter Sorger and Ilya Goldberg in 2000, and has helped direct the project ever since. As an open source, community-led consortium, OME is now the leading provider of software solutions for biological image management. Central to its success has been the development and uptake of OME-TIFF, a standard image format that can be used across a range of different microscopy platforms, Bio-Formats, the world-leading library for accessing image data stored in proprietary file formats, and OMERO, the world leading open source image data management platform.

Prof Swedlow said, "It is a great honour to accept this award. Our vision has always been to create a global standard for imaging software and the community that has grown up around the open source development is extraordinary. In reality I am receiving this award on behalf of a large group of extremely talented people who share a common commitment to innovation through teamwork, collaboration and the process of creating something new and exciting as a community. The support we have received from BBSRC, as well as the Wellcome Trust, during the early stages of the research has been invaluable."

Professor Swedlow also won the category prize for Social Innovator of the Year. He receives a £10,000 award as Innovator of the Year. He received his two awards from Mr David Willets, UK Minister of State for Universities and Science. Two other category prizes - Commercial Innovator and Most Promising Innovator - were won by Professor Chris Lowe from University of Cambridge and Professor Keith Waldron from the Institute of Food Research respectively, each receiving £5000 prize money.

Glencoe Software’s OMERO Data Management Engine: OME Open Source Technology Continues to Perform in Commercial Products

Seattle, November 22, 2010 – Glencoe Software Inc, a pioneer in biological research image and metadata management tools is pleased that PerkinElmer, Inc. a global leader focused on improving the health and safety of people and the environment has again chosen Glencoe Software’s open source-based tools as the foundation of its newly released Columbus® Scope cellular imaging software solution for microscopy. Columbus Scope allows researchers to read, visualize and re-analyze an unprecedented number of different vendor-specific research imaging file formats, save and use their experimental metadata parameters, and share images with their colleagues and collaborators.

The introduction of Columbus Scope for microscopy follows the very successful Columbus® Conductor and Columbus® Gallery data management systems for High Content Screening. All of these tools are based on the Open Microscopy Environment’s open source OMERO Platform, which provides access to large image datasets over standard internet connections for scientific visualization, analysis, and collaboration. A typical research microscopy facility will have seven to ten different microscope hardware and software acquisition systems, and often times 15-25 for the larger core microscopy facilities. The Open Microscopy Environment Consortium pioneered unique software engineering design principles that enable researchers to read and organize image data from all of these different systems. With OMERO scientists can access new methods of analyses and workflows, enhancing research in cancer, immunology, developmental biology and infectious diseases.

Jason Swedlow, President of Glencoe Software, and co-Founder of the Open Microscopy Environment, said, “We are pleased that PerkinElmer has chosen OMERO as the foundation of the newest member of the Columbus family of products. This is another successful example of the flexibility and power of OME’s software.”

Glencoe Software, Inc. is a member of the OME Consortium and provides commercial access and customization of OME resources. For more information, contact sales@glencoesoftware.com. Glencoe Software, Inc. is registered in the State of Washington, USA.

PerkinElmer® and Columbus® are registered trademarks of PerkinElmer, Inc.

Glencoe Software and the Open Microscopy Environment Release New Versions of the Pioneering Software, Bio-Formats and OMERO for Scientists

Seattle, November 22, 2010 – Glencoe Software Inc. , a leading provider of image data management tools for life science and biopharmaceutical research, and a member of the Open Microscopy Environment Consortium, is pleased to announce the next release of its flagship software packages, Bio-Formats, the world-leading image file translation tool, and OMERO, its image data management platform. These new versions include many important updates. Bio-Formats 4.2.1 now supports over 100 image file formats – newly supported formats include the PerkinElmer Densitometer format and a number of proprietary versions of TIFF. In OMERO Beta4.2.1, the speed of deleting very large datasets has been substantially improved and a series of improvements to the OMERO.web application have been released. The combined enhancements focus on productivity and performance within diverse workflow environments that require flexible interaction with other software platforms, collaborative interaction and careful cataloging control and management of scientific image-assets.

Jason Swedlow, President of Glencoe Software, Inc., and co-founder of OME, said “OME and Glencoe Software are excited about this latest release. Bio-Formats and OMERO are used globally by the scientific community, and we were determined to rapidly release these new facilities to enhance the experience of our user base where it counts. OME’s infrastructure has many possible applications, and we are proud of our ongoing contributions that enable access and sharing of critical original image data in research.”

The new releases represent the last major release of the 2010 calendar year. Swedlow, said, “Our work will now focus on support of very large images, and the further enhancement of our OMERO.fs filesystem access technology. We are very excited about this work and look forward to hearing feedback from our user community.” The OMERO.fs filesystem access technology streamlines image data handling from microscope acquisition to final storage and archiving – reducing image data volumes and redundancy in centralized database management decisions.

Glencoe Software and The Journal of Cell Biology Pioneer On-Line Publishing of Scientific Image Data: New Version of JCB DataViewer Released

Seattle, October 4, 2010 – Glencoe Software Inc. The Journal of Cell Biology (JCB), The Rockefeller University Press, and Glencoe Software are pleased to announce the release of the next version of the JCB DataViewer, the world’s first scientific image data publication system. First released in Dec 2008, the JCB DataViewer has been under continuous development to support new image data formats and provide new functionality for its users. Now, for the first time, scientists will be able to download the original image data associated with scientific articles published in The JCB.

The JCB DataViewer currently includes original image data (multi-dimensional image data taken directly from a microscope imaging platform) for 110 manuscripts. Liz Williams, Executive Editor of the Journal, said, “Submission of original image data by authors to the JCB DataViewer has been steadily increasing since its launch in 2008. The scientific community clearly appreciates the value of this resource, and we hope they will embrace the new download functionality in order to maximize its utility.”

The latest release allows JCB readers to download image data in OME-TIFF format, the open scientific image data format released by the Open Microscopy Environment (OME). This format is open, non-proprietary, and stores critical image metadata—information about the original imaging system and data acquisition parameters. This allows readers to access how the data included in a published paper were originally acquired and to re-analyze the data using their own software.

Mike Rossner, Executive Director of The Rockefeller University Press, said, “The JCB was founded by a group of scientists who needed a journal to showcase their micrographs with the highest quality reproduction. Our commitment to innovative presentation and sharing of image data continues today with the JCB DataViewer.”

Jason Swedlow, President of Glencoe Software, Inc., and co-founder of OME, said “OME and Glencoe Software are excited to be a part of this important development and milestone in scientific publishing. OME’s infrastructure has many possible applications, and we are proud of our ongoing contributions to the functionality enabling access and sharing of original image data in science.”

The Journal of Cell Biology is published by The Rockefeller University Press. All editorial decisions are made by active scientists in conjunction with in-house scientific editors. JCB content is available for free six months after publication. Authors retain copyright to their publications and third parties may reuse the content under a Creative Commons License.

Glencoe Software to Sell Licenses for OME's Open Source Bio-Formats Library

Seattle, November 25, 2008 - The Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin at Madison and Glencoe Software, Inc. are pleased to announce that Glencoe Software has been named as the exclusive provider of commercial licenses for the LOCI's popular Bio-Formats microscopy file format converter library. LOCI is one of the key members of the Open Microscopy Environment (OME) Consortium, a group of academic imaging laboratories dedicated to delivering great tools for biological imaging research. Bio-formats is open source software licensed under the GNU General Public License Version 3 (GPL) and is used in hundreds of laboratories around the world to read >60 proprietary image file formats. Glencoe Software is a member of the OME Consortium, a development partner in the Bio-formats project, and is dedicated to continued development of this important tool for the biological research community.

In announcing the agreement, LOCI Director, Kevin Eliceiri, said, "I am pleased to announce this agreement with Glencoe Software for commercial licensing of Bio-Formats. While we are dedicated to keeping the open source nature of Bio-Formats, this agreement ensures that commercial organizations can make use of Bio-Formats as well. This is consistent with our goal of making Bio-Formats available across the biological imaging community.”

Dr. Jason Swedlow, Founder and President of Glencoe Software, Inc., said "Bio-Formats is a critical resource for hundreds of users around the world, and we look forward to continuing our contributions to this important project. We are happy to help expand the delivery of Bio-Formats to the commercial imaging community. Bio-Formats licensing is just one more example of our dedication to supporting open source software for biological imaging and our continuing collaboration with the OME Consortium."