IFREMER is one of the world’s leading institutes in marine science and technology. It was founded in 1984 and is present on all the French and overseas seaboards, with laboratories located in 16 cities on French coasts as well as the overseas territory like New Caledonia, French Polynesia, French Guiana, Martinique, and Reunion Island. IFREMER works in the Indian, Atlantic and Pacific oceans and operates the French Oceanographic Fleet for the benefit of the national scientific community. IFREMER designs its own state-of-the-art vessels and equipment to explore and observe the ocean, from the coast to the open ocean and from the abyss to the interface with the atmosphere. IFREMER is a public establishment of industrial and commercial nature (EPIC), with a budget of about 240 million euros/year. It is placed under the joint supervision of the French ministries of Higher Education, Research and Innovation (MESRI), Ecological Transition and Solidarity (MTES) and Agriculture and Food (MAA). IFREMER thus invests in research of excellence based on various disciplines and themes and, to do so, relies on partnerships with universities and research organizations. It is also a driving force at the international and European levels for concerted programming initiatives, whether in terms of research or infrastructure (fleet, observatories, databases).

Need of IFREMER for a collaborative LIMS

IFREMER has more than 1 500 scientists who are studying marine samples, carrying out laboratory testing on hundreds of marine samples every day using a lot of various instruments. With more than 26 teams scattered around 23 different sites in the world, the top priority for IFREMER finding a LIMS that would ease its daily research activities by improving resource management (instruments, reagents samples) and facilitate collaboration between scientists and labs which was a real challenge. The LIMS must be able to manage all laboratories’ data (experiments, samples, results), equipment (instruments, devices), resources (reagents) and have them organized in one place for scientists to easily access and search particular records allowing them to collaborate and work together simultaneously. “Having to sort out and rearrange all of our confidential data and keeping it in one easily accessible software, that not only has the ability to be customizable but also highly secure and offers collaborative solutions, is important to us. And this is why we chose LabCollector” says Florian Nivert, Project manager for IFREMER

LabCollector LIMS Solution for IFREMER

LabCollector is a full-featured Laboratory Information Management Software (LIMS) dedicated to laboratory resource management. It is built on modules of data to store any kind of information and a technology stack of 20 add-ons dedicated to specific laboratory applications. IFREMER has embraced the digitalization of its laboratories using LabCollector LIMS modules and add-ons, and continues to enlarge its usage. IFREMER laboratories are using the inventory Modules of LabCollector such as Reagents and supplies, Instruments, Samples, Strains and Cells, Chemical structures, Animals, Plasmids, Primers, Sequences, Antibodies, Microarrays and Documents to store raw data and manage it. More than 20 specific datasets were built using Customs modules of LabCollector and designed by IFREMER scientists themselves to store thousands of specific records. LabCollector’s set of modules constitutes a complete database of unique resources and data for IFREMER and includes powerful searching, organization and sharing features to which hundreds of IFREMER scientists refer every day for their work. Inside each laboratory, the separation of data through Groups of users supports the necessary data management flexibility the scientists may need to correctly protect, organize and share their data within their laboratory. To complement inventory management in LabCollector modules, for each laboratory IFREMER has acquired specific sets of LabCollector add-ons to exactly fit the local functional needs of its scientists:

ELN Add-on (Electronic Lab Notebook) is a complete replacement for the paper laboratory notebook and provides the versatility to fully record all experiments and keep years of work in a secure place using a user-friendly web interface. LabCollector ELN Add-on allows the IFREMER scientist to fully digitalize, organize, share and protect their experiments and results via a web browser (Chrome, Edge, Firefox, Safari) on a desktop, tablet or mobile phone inside or outside their lab.

Scheduler Add-on is a complete reservation tool dedicated to the management of the laboratory equipment for the scientific teams of IFREMER. The Scheduler Add-on allows them to search for available equipment, schedule reservations, visualize available instruments and usage, easily identify free and used instruments in an outlook-style calendar, extract and display usage statistics through friendly dashboards. The Scheduler add-on really eases the daily life in the laboratories while being an essential tool for the efficient management of hardware resources at IFREMER.

Photobank Add-on is the LabCollector tool dedicated to the storage and organization of media files, at IFREMER it is used to keep pictures of the multiple fish species encountered during scientific campaigns on diverse oceans: images are uploaded in many different formats into LabCollector, classified by directories and annotated with metadata for an efficient classification and documentation of fish species. The images stored in the Photobank Add-on of IFREMER constitute an important database of the diversity of the marine ecosystem of our planet.

Aquarium Add-on is dedicated to the management of fish breeding facilities at IFREMER. It is used by scientists to manage fish entries, transfers & exits from tanks, and follow the complete life cycle of each fish, including growth and feeding. LSM Add-on (Lab Service Manager) is used at IFREMER for the management of routine tests done on samples collected during sea campaigns. With a very structured but flexible approach to test management, each sample is correctly traced with a complete guarantee of traceability of test results entry.

Query-Builder Add-on is used by IFREMER to leverage all the potential of massive data entry and storage in LabCollector modules. Because extracting complex data from a large database like IFREMER’s can be complex for scientists without IT knowledge, Query-Builder Add-on is used as a simple tool to create database queries with a visual web editor online and turn LabCollector into a real-time data source for further analysis with only a few clicks. All IFREMER scientists can easily find and export complex relational datasets from LabCollector in real time for statistical analysis or reporting purposes.

LabCrossSearch is a new application under implementation at IFREMER dedicated to leveraging the full benefits of searching data of multiple labs of a large and complex research organization like IFREMER through one single and easy-to-use search engine. It allows scientists to easily share the exact data they want with other team members in the other labs of IFREMER. Built as a simple but powerful search bar on a web page, LabCrossSearch allows authorized personnel of IFREMER to search for reagents and supplies, instruments, samples, strains and cells, chemical structures, animals, plasmids, primers, sequences, antibodies, microarrays, documents or any custom data contained in LabCollector modules of multiple IFREMER laboratories with a single text query. LabCrossSearch leverages the full collaborative potential of scientists at IFREMER. IFREMER is also using other LabCollector Add-ons like Sample Receiving Add-on to manage and speed up the receiving and storage of hundreds of samples in plates & boxes with quality control processes for each sample.

The Workflow Add-on has been introduced into the IFREMER LabCollector ecosystem to orchestrate some complex laboratory data processes. With a built-in graphical flow chart designer using the mouse in a friendly web user interface, the Workflow add-on allows IFREMER scientists to build and execute their own data management processes according to their internal procedures, thanks to its modeling power. “The main advantage for us is that LabCollector LIMS allows IFREMER to have an efficient mutualization within our laboratories. We use different modules for each expertise and the possibility of having a link between each one of them is mandatory for us. LabCollector helps us valorize all obtained data” says Florian Nivert, Project manager for IFREMER.

Result: Success of IFREMER’s digitalization with LabCollector

IFREMER has now been using LabCollector since 2011 with more than 900 users across 26 different laboratories located all around the world. With LabCollector IFREMER illustrates a successful digitalization of a large academic research organization with one of the top collaborative web LIMS and ELN. Supported by a strong commitment of AgileBio in terms of technical support to IFREMER and reactivity to the expressed needs of its scientists, the relationship between AgileBio and IFREMER is strongly organized and maintained by the LIMS project leader for IFREMER, Florian Nivert, and throughout the years we’ve built a strong and efficient partnership.

Today, IFREMER is continuingly transitioning to the LabCollector system. Scientists use it daily and benefit from collaborative tools. Having access to clear and organized data for more than a decade is one of the reasons why IFREMER continue to expand LabCollector usage within all its laboratories. We are constantly in communication with the support team for any upcoming updates, training and feedback that we may have, thanks to their availability and quick response, we can see how LabCollector grows and improves on a daily basis. So far, IFREMER is fully satisfied with LabCollector as it continuously provides us with great solutions for our needs. Florian Nivert, Project manager for IFREMER