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Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The integration of resources and the sharing of knowledge across organisations enable scientific discoveries to be accelerated by increasing the productivity of laboratories, optimising funding efficiency, and addressing emerging global challenges. This paper presents a novel framework for digitalising and automating the administration of research laboratories through The World Avatar, an all-encompassing dynamic knowledge graph. This Digital Laboratory Framework serves as a flexible tool, enabling users to efficiently leverage data from diverse systems and formats without being confined to a specific software or protocol. Establishing dedicated ontologies and agents and combining them with technologies such as QR codes, RFID tags, and mobile apps, enabled us to develop modular applications that tackle some key challenges related to lab management. Here, we showcase an automated tracking and intervention system for explosive chemicals as well as an easy-to-use mobile application for asset management and information retrieval. Implementing these, we have achieved semantic linking of BIM and BMS data with laboratory inventory and chemical knowledge. Our approach can capture the crucial data points and reduce inventory processing time. All data provenance is recorded following the FAIR principles, ensuring its accessibility and interoperability.

Modern investigations in biology often require the efforts of one or more groups of researchers. Often these are groups of specialists from various scientific fields who generate and share data of different formats and sizes. Without modern approaches to work automation and data versioning (where data from different collaborators are stored at different points in time), teamwork quickly devolves into unmanageable confusion. In this review, we present a number of information systems designed to solve these problems. Their application to the organization of scientific activity helps to manage the flow of actions and data, allowing all participants to work with relevant information and solving the issue of reproducibility of both experimental and computational results. The article describes methods for organizing data flows within a team, principles for organizing metadata and ontologies. The information systems Trello, Git, Redmine, SEEK, OpenBIS and Galaxy are considered. Their functionality and scope of use are described. Before using any tools, it is important to understand the purpose of implementation, to define the set of tasks they should solve, and, based on this, to formulate requirements and finally to monitor the application of recommendations in the field. The tasks of creating a framework of ontologies, metadata, data warehousing schemas and software systems are key for a team that has decided to undertake work to automate data circulation. It is not always possible to implement such systems in their entirety, but one should still strive to do so through a step­by­step introduction of principles for organizing data and tasks with the mastery of individual software tools. It is worth noting that Trello, Git, and Redmine are easier to use, customize, and support for small research groups. At the same time, SEEK, OpenBIS, and Galaxy are more specific and their use is advisable if the capabilities of simple systems are no longer sufficient.

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.

Through the study and analysis of a precise economic sector, that of agribusiness, this contribution attempts to elaborate a replicable conceptual model that, in compliance with scientific methodologies, can contribute to the development of current archives, which will later be historical, capable of managing traceable and secure digital flows. In that absolute semantic individuality that characterizes each documentary complex, subject to "rules" of treatment only by productive affinities and common provenance characteristics, the application of standards has been a matter of discussion for the scientific literature. The example from which we wish to move concerns a specific category of Software Packages (LIMS) that are currently used in Italy by analytical laboratories and that implement integrated management of multiple data and processes.

Continuous progressive wheel resulted in scattered plans of the major objective to climb the ladder of success within a very short period of time. Within past years, Electronic Health Records (EHR) have been realized due to the growing number of hospitals worldwide. EHR systems can be in different forms, that refer to a wide range of electronic information systems used in healthcare. Medical institutions that might use EHRs are hospitals, pharmacies, general surgery practices, and other health care professionals. Clinical or medical coding is an important process to transform medical documents such as laboratory or radiologic results beside physician notes into universal alphanumeric codes that represents the medical diagnosis, procedure, service, or equipment. As archiving process is an important part of the clinical lab, besides searching for related information or previous tests’ results are boring work and in order to make this process easier, faster and accurate, this paper proposed the design and implementation of a web-based clinical laboratory management system, in which only authorized systems’ users such as lab assistant or physician can access patients’ records in order to ensure that the whole process is secure, accurate and reliable. This system is developed using MySQL for database design and PHP, html, CSS and JavaScript for user interfaces.

Abstract Background Well-characterized biomaterials of high quality have great potential for acceleration and quality improvement in translational biomedical research. To improve accessibility of local sample collections, efforts have been made to create central biomaterial banks and catalogues. Available technical solutions for creating professional local sample catalogues and connecting them to central systems are cost intensive and/or technically complex to implement. Therefore, the Translational Thematic Unit HIV of the German Center for Infection Research (DZIF) developed a Laboratory Information and Management System (LIMS) called HIV Engaged Research Technology (HEnRY) for implementation into the Translational Platform HIV (TP-HIV) at the DZIF and other research networks. Results HEnRY is developed at the University Hospital of Cologne. It is an advanced LIMS to manage processing and storage of samples and aliquots of different sample types. Features include: monitoring of stored samples and associated information data selection via query tools or Structured Query Language (SQL) preparation of summary documents, including scannable search lists centralized management of the practical laboratory part of multicentre studies (e.g. import of drawing schemes and sample processing steps), preparation of aliquot shipments, including associated documents to be added to shipments unique and secure identification of aliquots through use of customizable Quick Response (QR) code labels directly from HEnRY support of aliquot data transmission to central registries. In summary, HEnRY offers all features necessary for a LIMS software. In addition, the structure of HEnRY provides sufficient flexibility to allow the implementation in other research areas. Conclusion HEnRY is a free biobanking tool published under the MIT license. While it was developed to support HIV research in Germany, the feature set and language options, allow much broader applications and make this a powerful free research tool.

The signatures of element isotope fractionation can be used for the indirect identification of extant or extinct life on planetary surfaces or their moons. Element isotope fractionation signatures are very robust against the harsh environmental conditions, such as temperature or irradiation, which typically prevail on solar system bodies. Sulphur is a key element for life as we know it and bacteria exist, such as sulphur reducing bacteria, that can metabolize sulphur resulting in isotope fractionations of up to −70‰ δ34S. Geochemical processes are observed to fractionate up to values of −20‰ δ34S hence, fractionation exceeding that value might be highly indicative for the presence of life. However, the detection of sulphur element isotope fractionation in situ, under the assumption that life has existed or still does exist, is extremely challenging. To date, no instrument developed for space application showed the necessary detection sensitivity or measurement methodology for such an identification. In this contribution, we report a simple measurement protocol for the accurate detection of sulphur fractionation δ34S using our prototype laser ablation ionization mass spectrometer system designed for in situ space exploration missions. The protocol was elaborated based on measurements of five sulphur containing species that were sampled at different Mars analogue field sites, including two cave systems in Romania and the Río Tinto river environment in Spain. Optimising the laser pulse energy of our laser ablation ionization mass spectrometer (LIMS) allowed the identification of a peak-like trend of the 34S/32S ratio, where the maximum, compared to internal standards, allowed to derive isotope fractionation with an estimated δ34S accuracy of ∼2‰. This accuracy is sufficiently precise to differentiate between abiotic and biotic signatures, of which the latter, induced by, e.g., sulphate-reducing microorganism, may fractionate sulphur isotopes by more than −70‰ δ34S. Our miniature LIMS system, including the discussed measurement protocol, is simple and can be applied for life detection on extra-terrestrial surfaces, e.g., Mars or the icy moons like Europa.

Cloud computing is providing cheaper, cost effective efficient automation, data management services to the organizations and this trend is gradually increasing. Using cloud based services can eliminate cost and complexity of managing the underlying application. It allows users to access and use the most sophisticated technologies without being required to pay enormous amounts of money to purchase the system or to develop it in-house. This study aimed to investigate cloud computing advantages and disadvantages, its services and implementation stages in pharmaceutical industry of Pakistan. Cloud computing practices included Cost Saving, Security & Privacy, Automation, Data Integrity, and Regulatory compliance. An Adopted survey was planned and circulated over an example of 400 workers. Research hypotheses were evaluated using structured equation modelling. The outcome shows that cost savings, security and privacy, competitive pressure, automation and awareness have a positive and fundamental effect on pharmaceutical operations. Strangely, there is a negative effect of external support on cloud computing. The effects are noticeable in the pharmaceutical industry.

Spectroscopic instruments were a part of payloads on orbiter and lander missions and delivered vast data sets to explore minerals, elements and molecules on air-less rocky planets, asteroids and comets on global and local scales. To answer current space science questions, the chemical composition of planetary rocks and soils at grain scale is required, as well as measurements of element (isotope) concentrations down to the part per million or lower. Only mass spectrometric methods equipped with laser sampling ion sources can deliver the necessary information. Laser sampling techniques can reduce the dimensions of the investigated sample material down to micrometre scale, allowing for the composition analysis of grain-sized objects or thin mineral layers with sufficiently high spatial resolution, such that important geological processes can be recognised and studied as they progressed in time. We describe the performance characteristics, when applied to meteorite and geological samples, of a miniaturised laser ablation/ionisation mass spectrometer (named LMS) system that has been developed in our group. The main advantages of the LMS instrument over competing techniques are illustrated by examples of high spatial (lateral and vertical) resolution studies in different meteorites, terrestrial minerals and fossil-like structures in ancient rocks for most elements of geochemical interest. Top-level parameters, such as dimension, weight, and power consumption of a possible flight design of the LMS system are presented as well.

Continuous progressive wheel resulted in scattered plans of the major objective to climb the ladder of success within a very short period of time. Within past years, Electronic Health Records (EHR) have been realized due to the growing number of hospitals worldwide. EHR systems can be in different forms, that refer to a wide range of electronic information systems used in healthcare. Medical institutions that might use EHRs are hospitals, pharmacies, general surgery practices, and other health care professionals. Clinical or medical coding is an important process to transform medical documents such as laboratory or radiologic results beside physician notes into universal alphanumeric codes that represents the medical diagnosis, procedure, service, or equipment. As archiving process is an important part of the clinical lab, besides searching for related information or previous tests’ results are boring work and in order to make this process easier, faster and accurate, this paper proposed the design and implementation of a web-based clinical laboratory management system, in which only authorized systems’ users such as lab assistant or physician can access patients’ records in order to ensure that the whole process is secure, accurate and reliable. This system is developed using MySQL for database design and PHP, html, CSS and JavaScript for user interfaces.

The field of ancient genomics has undergone a true revolution during the last decade. Input material, time requirements and processing costs have first limited the number of specimens amenable to genome sequencing. However, the discovery that archeological material such as petrosal bones can show increased ancient DNA preservation rates, combined with advances in sequencing technologies, molecular methods for the recovery of degraded DNA fragments and bioinformatics, has vastly expanded the range of samples compatible with genome-wide investigation. Experimental procedures for DNA extraction, genomic library preparation and target enrichment have become more streamlined, and now also include automation. These procedures have considerably reduced the amount of work necessary for data generation, effectively adapting the processing capacity of individual laboratories to the increasing numbers of analyzable samples. Handling vast amounts of samples, however, comes with logistical challenges. Laboratory capacities, equipment, and people need to be efficiently coordinated, and the progress of each sample through the different experimental stages needs to be fully traceable, especially as archeological remains of animals or plants are often provided and/or handled by many different collaborators. Here we present CASCADE, a laboratory information management system (LIMS) dealing with the specificities of ancient DNA sample processing and tracking, applicable by large and small laboratories alike, and scalable to large projects involving the analysis of thousands of samples and more. By giving an account of the specimen’s progress at any given analytical step, CASCADE not only optimizes the collaborative experience, including real-time information sharing with third parties, but also improves the efficacy of data generation and traceability in-house.

Center of Pharmaceutical Analytics purchased and installed LabWare LIMS laboratory information system, LabWare ELN electronic laboratory journals from LabWare company. At the moment, the system is integrating into the work of the laboratory, templates for research work are created and employees are trained. The article opens a series of articles of the integration of the LIMS system into the work of the analytical center. LabWare has received universal recognition, is a leader in the global market of global Laboratory information systems (LIMS) and has a wide range of loyal users.

This article describes the results of Laboratory Information Management System implementation in an expert institution dealing with medicines evaluation. The purpose of the study was to evaluate the feasibility of providing digital support to the laboratories of the Federal State Budgetary Institution «Scientific Centre for Expert Evaluation of Medicinal Products» of the Ministry of Health of the Russian Federation and to assess the functionality of the information system in terms of coverage of functional capabilities of various classes of laboratory software. The implementation of laboratory automation systems is required by the current regulations and is in line with international approaches to organisation of the quality management. The information system implementation made it possible to computerize management of drug samples, distribution of assignments among responsible employees, storage and management of documents, and reporting of test results. It created opportunities for direct integration with laboratory equipment allowing for creation of analytical protocols without manual data transfer. The implemented solution meets all requirements and standards for the functional capabilities of laboratory information systems. A similar system could be used in chemical, pharmacological, medical and biochemical laboratories, its implementation will make it possible to meet both national and international standards. These innovations are part of the concept of CALS/PLM technologies integration into institutions management programmes.

Nowadays, cell-based assays are an elementary tool for diagnostics, animal-free substance testing and basic research. Depending on the application, the spectrum ranges from simple static cell cultures in microtiter plates to dynamic co-cultures in complex micro physiological systems (organ-on-a-chip). Depending on the complexity of the assay, numerous working steps have to be performed and the data from different analysis systems have to be processed, combined and documented. A universal platform has been developed for the automated handling of cell-based assays, which combines a laboratory information management system (LIMS) with a laboratory execution system (LES), a universal laboratory automation platform and established laboratory equipment. The LIMS handles the administration of all laboratory-relevant information, the planning, control and monitoring of laboratory processes, as well as the direct and qualified processing of raw data. Using a kidney-on-achip system as an example, the realization of complex cellbased assays for the animal-free characterization of the toxicity of different antibiotics will be demonstrated. In the kidney-on-a-chip system the artificial proximal tubular barrier was formed by seeding human immortalized proximal tubule cells (RPTEC) and human blood outgrowth endothelial cells (BOEC) on ThinCert™ membranes. Transepithelial electrical resistance (TEER) was measured daily to evaluate the barrier function of the cellular layers. Fluid handling and TEER measurements were performed using a laboratory automation platform that communicates directly with the LIMS. The LES supports laboratory assistants in executing the manual handling steps of the experiments.

Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research. Best-practice guidelines have been adapted to align with a low-resource setting and have been instrumental in the development of a quality-management system, including standard operating procedures and a quality-control regimen. Here, we provide a summary of 10 important considerations for initiating and establishing an academic research biobank in a low-resource setting. These include addressing ethical, legal, technical, accreditation and/or certification concerns and financial sustainability.

Information Management Systems are the central process management and communication hub for many newborn screening programs. In late 2014, Newborn Screening Ontario (NSO) undertook an end to end assessment of its information management needs which resulted in a project to develop a flexible IS Information Systems (IS) ecosystem and related process changes. This enabled NSO to better manage its current and future work-flows and communication needs. An idealized vision of a Screening Information Management System (SIMS) was developed that was refined into enterprise and functional architectures. This was followed by the development of technical specifications, user requirements and procurement. In undertaking a holistic full product lifecycle redesign approach, a number of change management challenges were faced by NSO across the entire program. Strong leadership support and full program engagement are key for overall project success. It is anticipated that improvements in program flexibility and the ability to innovate will outweigh the efforts and costs.

The Lab Information Indexing System (LIIS) is a web-driven database application for laboratories looking to store their sample or culture metadata on a central server. The design was driven by a need to replace traditional paper storage with an easier to search format, and extend current spreadsheet storage methods. The system supports the import and export of CSV spreadsheets, and stores general metadata designed to complement the environmental packages provided by the Genomic Standards Consortium. The goals of the LIIS are to simplify the storage and archival processes and to provide an easy to access library of laboratory annotations. The program will find utility in microbial ecology laboratories or any lab that needs to annotate samples/cultures.

NMR spectroscopy is certainly the analytical methodology that provides the most information about a molecule but the long-term vision of this information is often lacking. We present here two innovative tools accessible free from the web. NMR assigner allows a chemical structure to be assigned to the corresponding NMR spectrum by simply drawing lines between atoms and automatically characterized signals. NMR resurrector allows NMR spectra to be recreated from published in-line experimental parts enabling the recovery of this lost knowledge.

Abstract Background A large number of different plant lines are produced and maintained in a typical plant research laboratory, both as seed stocks and in active growth. These collections need careful and consistent management to track and maintain them properly, and this is a particularly pressing issue in laboratories undertaking research involving genetic manipulation due to regulatory requirements. Researchers and PIs need to access these data and collections, and therefore an easy-to-use plant-oriented laboratory information management system that implements, maintains and displays the information in a simple and visual format would be of great help in both the daily work in the lab and in ensuring regulatory compliance. Results Here, we introduce ‘Phytotracker’, a laboratory management system designed specifically to organise and track plasmids, seeds and growing plants that can be used in mixed platform environments. Phytotracker is designed with simplicity of user operation and ease of installation and management as the major factor, whilst providing tracking tools that cover the full range of activities in molecular genetics labs. It utilises the cross-platform Filemaker relational database, which allows it to be run as a stand-alone or as a server-based networked solution available across all workstations in a lab that can be internet accessible if desired. It can also be readily modified or customised further. Phytotracker provides cataloguing and search functions for plasmids, seed batches, seed stocks and plants growing in pots or trays, and allows tracking of each plant from seed sowing, through harvest to the new seed batch and can print appropriate labels at each stage. The system enters seed information as it is transferred from the previous harvest data, and allows both selfing and hybridization (crossing) to be defined and tracked. Transgenic lines can be linked to their plasmid DNA source. This ease of use and flexibility helps users to reduce their time needed to organise their plants, seeds and plasmids and to maintain laboratory continuity involving multiple workers. Conclusion We have developed and used Phytotracker for over five years and have found it has been an intuitive, powerful and flexible research tool in organising our plasmid, seed and plant collections requiring minimal maintenance and training for users. It has been developed in an Arabidopsis molecular genetics environment, but can be readily adapted for almost any plant laboratory research.