Examples of LIMS systems used for crystallography | LIMS | Key features | URL | References | | Developed at EMBL, providing, as a remote service, automated communication between crystallization-setup and synchrotron data-collection facilities, enabling uninterrupted information flow over the whole sample cycle from pure protein to diffraction data | | Cornaciu (2021 ) | | Used in home laboratories and crystallization facilities to monitor crystallization results and to record all information from crystallization via data collection at synchrotrons to structure deposition and publication | | Daniel (2021 ) | | Used at European synchrotrons to collect information from users concerning their crystals and to provide the results of the data collection and data processing by the beamline to users | | De Maria Antolinos (2015 ); Delagenière (2011 ); Fisher (2015 ) | | Software to monitor the crystallization experiments performed by Formulatrix crystallization-drop imaging systems | | — | | LIMS to manage data at Argonne National Laboratory and capture data from cloning to crystallization | | — | | 2.1. Managing proteins and projects in a LIMSA basic requirement of a protein crystallography LIMS is that it should record the protein sequence being worked on, along with the various constructs used to express the typically recombinant proteins and protein fragments. The LIMS should also handle assemblies consisting of multiple proteins of a hetero-oligomer. To enable the tracking of metadata for ligand-binding studies, for example for studies of enzyme catalysis and drug discovery, the LIMS should have the possibility of tracking the ligands used for co-crystallization and soaking, at least at the level of notes. All of the subsequent steps of the workflow will be tied back to this basic information on the experimental setup. It is likely that some access restrictions to the information will be needed beyond a simple login, both to prevent unauthorized access to confidential work and to eliminate clutter. In IceBear , these requirements are met by organizing the work into `projects'; we recommend, but do not require, that each protein be placed into its own dedicated project. Each protein has an acronym and one or more sequences provided by the project owner. Users are organized into groups, which are then granted read-only or full access to a project. Project handover from a leaving researcher to a new project member is easily achieved by assigning the new researcher the access rights to the appropriate project. 2.2. Keeping track of crystallization trialsIn commercial and in-house crystallization screens the chemicals are currently not listed in a standardized format and this may limit some possible analysis later, which could become a future development target. A ligand may have been introduced to the protein prior to the experiment or added to the drops later, and this crystal-treatment information may be provided by the scientist. IceBear provides the flexibility to also handle this information as notes, allowing the users to define a chemical, for example an in-house inhibitor, by an identification code. IceBear includes information on crystallization plate types and knows the incubation temperature of the imager. Monitoring of the crystallization drops is performed by visual inspection for days, weeks or even months. Automatic imaging of crystallization plates naturally makes this task easier for the scientists who inspect the drops, and who can also score the drops into different categories to keep track of the most promising conditions, and in the ideal case indicates in the LIMS the drops in which crystals are present. Scoring at least the best images in each inspection is recommended; not only does this highlight the wells with crystals in the plate overview, but also allows plates to be sorted by best score. IceBear connects to the image stores and databases of automated imagers to import inspections as they occur. For smaller laboratories without imaging hardware, it is still important to preserve and organize microscope images. IceBear can work entirely without images if need be, but also allows the user to attach manually captured images obtained from a microscope. The times of the first and subsequent imaging events are recorded, allowing users to view time-lapsed, low-frame-rate movies of crystal growth using either visible or UV images. 2.3. Crystal harvestingOnce crystals have grown, they are harvested either (i) directly via a cryocooling protocol and subsequent mounting on a pin or (ii) first used for a ligand-soaking experiment, followed by cryocooling and mounting on a pin. At this stage a unique sample name for each crystal needs to be generated. In most laboratories, crystal cryoprotection and mounting on a pin is still an entirely manual process. Cryocooling of the fished crystals is often carried out on a cramped bench near liquid nitrogen. Therefore, any LIMS work, such as specifying the drop from which the crystal is harvested and the pin barcode and/or its position in the puck and in the dewar, needs to be minimized while preserving the chain of custody. IceBear has a minimal but highly functional crystal-fishing interface that is optimized for use with a 2D barcode scanner to enter the bar codes of the pins, pucks and dewars into a database and drag–drop operations on a touch screen. Researchers can add detailed notes at this point, but to facilitate the process commonly used remarks can also be added with a single touch. The simplicity of the default workflow is intended to drive user compliance, ensuring that crystal harvesting is recorded correctly and enabling the subsequent submission of accurate shipment information. 2.4. Sending a shipment to the synchrotron2.5. data collection, data processing and structure solution at the synchrotron. | Making notes when collecting data. Notes can be captured immediately and are associated with the crystal. `Quick notes' buttons allow commonly used notes to be added easily. | | Retrieval of metadata as a new feature in . ( ) Details of the experimental setup for data collection, including the location of the raw data and details of the beamline used. ( ) List of data sets obtained from crystals of a shipment, sorted from high to low resolution. For each data set the icons provide the link to its crystal page and its project page (in the database), as well as to its crystal page and its shipment page. | 2.6. Deposition of the crystal structure | The crystal page of is its central hub, with pointers to the construct used, the crystallization and crystal-treatment information, the PDB and the location of the raw data set. The files option allows, for example, the archiving of important log files relevant to this crystal. The notes are generated either by (for example when a crystal is harvested and when a crystal is shipped) or by the user (at any point). The crystal page of a crystal can be found by using the search option (top right), for example by specifying its PDB code ( ; Sridhar , 2020 ) or its sample name. The top left icons are navigation tools to find the plate and project information. The question mark (top right) provides context-specific help information. | The raw data are critical information that must be preserved. IceBear , by default, stores the relevant ISPyB link on the crystal page, but also allows the notification of other storage locations on its crystal page. While in theory the data could be uploaded directly into the LIMS and attached to the protein of interest, common practice is either to leave it in place at the synchrotron or to archive it on other IT infrastructures, with both options being more suited than the LIMS for the long-term archival of large quantities of data. Either way, the location of these raw data needs to be recorded in the LIMS to allow retrieval and access later. A further risk with any IT-based system is that the product becomes unsupported, leaving researchers' data locked in a proprietary legacy system with no realistic prospect of migration to a replacement. This scenario has been specifically considered from the beginning of IceBear development, both in licensing and in the choice of supporting technologies. IceBear is made available as open-source software under the MIT License, which specifically grants the right to modify and redistribute the software. It runs on the industry-standard `LAMP stack' (Linux, Apache, MySQL, PHP) and uses the minimum amount of third-party code, aiming to maximize future maintainability by minimizing the specialist knowledge required. The ongoing work to improve the adherence of IceBear to FAIR data principles will make it easier to migrate the data stored therein to any future replacement system. The metadata-exchange protocols between the home laboratory and synchrotron will make it possible to extend the metadata that are sent from the home-laboratory LIMS to the synchrotron ISPyB with sequence, structure and ligand information. This information is required by the downstream structure-solution and structure-analysis pipelines in place at several synchrotrons and therefore these extensions will allow the best use of the impressive quantity of metadata that is generated by the synchrotrons. AcknowledgementsWe thank the University of Oulu local IceBear user community for daily feedback and for acting as crash test dummies for the latest IceBear updates and features. The national facilities Instruct-ERIC Centre Finland and the FINStruct Biocenter Finland platform are acknowledged for their continuous support of IceBear and for feature suggestions from the facility point of view. We thank the ISPyB developer community, specifically Ana Gonzalez, Jie Nan and Alberto Nardella at the MAX IV synchrotron, for their help with the latest ISPyB integration features. We also thank the IT staff of the University of Oulu, especially Jesse Korhonen, for help in setting up the backup system and hosting instances of IceBear . Funding informationThe development of IceBear was funded by Biocenter Oulu and Research Council of Finland (grant No. 345512 to LL). The cloud version of IceBear , IceBox , was developed with support from the EOSC-Life project and received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 824087. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence , which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. Follow Acta Cryst. D | |
|
IMAGES
VIDEO
COMMENTS
Project management is a discipline of planning, controlling, securing and organizing resources to attain specific objectives. A project can be perceived as an impermanent endeavour with a defined starting and end, undertaken to convene unique objectives and goals, normally to bring about useful change. The impermanent nature of projects differs ...
Project management is the use of specific tools, methods, skills to complete a project. In its foundation are the efforts to create value through the final result. A project usually has a team, a schedule, a budget, and set goals and expectations. It is a temporary and progressive attempt to reach a specific objective.
13 essay samples found. An essay on project management can provide insights into the principles and practices of effective project planning and execution. It can discuss project management methodologies, tools, and the skills required for successful project leadership, emphasizing the importance of project management in various industries and ...
Project Management February J. 2014 A project is a temporary group of activity designed to produce unique products and services or results. Typically, a project has a defined beginning and end and therefore having defined scope and resources. (Pierre, 2012). A project also has a specific set of operations to accomplish a singular goal.
1 page / 653 words. The project management life cycle includes five high-level phases that account for all aspects of managing a project from beginning to end. These five phases are: initiating, planning, executing, monitoring and controlling, and closing. Having an understanding of the parts of each phase, and ensuring...
Browse essays about Project Management and find inspiration. Learn by example and become a better writer with Kibin's suite of essay help services. Essay Examples
The main elements of the effective project management are resource scheduling, budgeting and cost control, teamwork and leadership.. The book A Guide to the Project Management underlines that the main characteristics of projects are: "performed by people, constrained by limited resources and planned, executed and controlled" (2000, p. 4).
27 September 2021by Essay Sauce. Project management can be defined as the knowledge, skills, methods required to perform a set of tasks which are carried out by a group of individuals working towards a common objective. Project management highlights risks, cost, scope, time and quality in a project. According to me, Project management plays a ...
The Relationship Between Project Management and Company Performance. Abstract: In this paper, we focus on the significance of project management and correlation between project management and the success of the organization. Background: The problems in multi-project companies are inherently complex and need to be addressed systematically.
A program is a group of an inter-related project run together to achieve efficiency in a project that can't be achieved by running individually (Meredith, 2017). It helps in risk mitigation, the economics of scale, easy management. A project may or may not be a part of a program whereas a program must be a project.
Project Management Essays. Importance of Operations Research in Organizations. ... Overview Version control is the backbone of software development, establishing project management and teamwork. The changes in codes are, therefore, systematically documented by the tool over time, as Beckman et al. (2021) noted. ... For research and sample use only.
Essay on Project Management Process. Published: 2021/12/02. Number of words: 3946. Abstract. Project management is a tool used to ensure maximum utilization of goods and resources available to achieve specific goals of a project. The main objective of this paper is to show how project management plays an important role in ensuring the project ...
Management. Project management is the planning, organizing and managing of tasks and resources to accomplish a defined objective, usually with constraints on time and cost. Most projects, whether they are large and complex or small and simple, can be planned by breaking the project into small, easily manageable tasks, scheduling the tasks, and ...
Project Management essay example for your inspiration. ️ 2897 words. Read and download unique samples from our free paper database.
To manage a project effectively, the managing team should make plans, organize them and control the resources to realize the set objectives. Every project has a beginning and an end (Maylor 2005, p. 154). An order process can also be taken as a project with set objectives, a start and an end. Get a custom Essay on Project Management Process.
Project Management Essay: Conclusion. In summary, this paper examined project design, activity network diagram, and customer influence on the project design. It also discussed the earliest start dates, latest finish dates, critical paths with illustrations and lead time price relationship in detail. Throughout the article, it is evident that ...
Project Management - Free Essay Examples and Topic Ideas. Project management is the process of planning, organizing, directing, and controlling resources such as people, time, and budget to achieve specific goals and objectives in a project. It involves identifying project requirements, developing a project plan, executing the plan, monitoring ...
Project Management Planning of Office Relocation. Example essay. Last modified: 22nd Sep 2021. The main purpose of this project in hand is to offer goods to customers in an quick manner by deploying less time and reduction over the expenses. This will prove to be fruitful for Nisa Ltd as service and timely delivery of products over shops will ...
A project management plan includes all actions necessary to define, integrate, and coordinate all subsidiary and complementing plans into a cohesive project management plan. It defines how the project is executed, monitored and controlled, and closed. The project management plan is updated and revised through the integrated change control process.
Question 1. 1.1 Project. A Project can be defined as a complex human endeavour to create change with in a set budget and time to provide specific goals and out comes that is unique to an organisation. 1.2 Project Management. Project Management is a set of principles to effectively manage the process and activity of planning, organizing ...
2230 Words. 9 Pages. 5 Works Cited. Open Document. Project Management. In today's business it is in the best interest of companies to have project managers. Common sense isn't always easily accomplished. Anyone who's ever worked on a project in a technical setting knows this. Indeed, much of working with others consists of solving unexpected ...
A Case Study - 692 Words | Essay Example. Project Management. A Case Study Essay. The connection with the customer and their experience is an essential business driver in ensuring the organization's project purposes are achieved. They are the most critical stakeholders in project managers' projects. On the other hand, the team's ...
Project 2025 is led by the Heritage Foundation. It does not directly come from Mr. Trump. But that's only part of the story. Portions of the plan were driven by people who were top advisers to ...
Project Manager. While project management is a structured process of planning, execution, control, monitoring, and termination of a project, a project manager is a person who plays a leading role at all these stages. Being a leader of a team, a project manager ensures the cooperation of its members for appropriate outcomes within the framework ...
1. Introduction. Protein crystallography has impacted our understanding of biological processes, making it possible to carry out structure-based drug discovery and enabling the development of artificial intelligence methods to predict protein structures with high precision (Jumper et al., 2021).The latter is a result of decades-long tradition and the requirement for researchers to deposit ...