BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

BackgroundMaking forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.<br/

Calendering of freeze-cast MXene aerogel

A calender press is calibrated to achieve accurate aerogel thicknesses post-compression. For full experiment details and details of attached data see .pdf

Freeze-casting of Ti3C2 MXene suspension I

Freeze-casting of Ti3C2Tz aqueous nanoparticle suspensions to give well-aligned nanoparticles in a sample within the target dimensions and tolerances. For full details of the experiment and attached images see the uploaed .pdf

Dynamic Light Scattering (DLS) for nanoparticle size-distribution acquisiton V

Particle size distributions (PSDs) of liquid cascade centrifugation (LCC)-fractionated Ti3C2 MXene nanoparticles in aqueous suspension are produced using DLS. Full PSDs are reconstructed via concentration tracking, such that non-LCC and LCC suspensions of the same synthesis product can be compared. For full experimental details and a description of provided data, see the attached .pdf

Partial Bay Elevation and Structure Section Model (Wei Feng)

2024 Model of a Partial Bay Elevation

Microanalysis of MXene synthesis products I

The composition of Ti3C2Tz synthesis products and sediments are obtained using microanalytical techniques.For full detail of the experiment conducted and uploaded data, please see the attached .pdf

Dynamic Light Scattering (DLS) for nanoparticle size-distribution acquisiton II

Identification of optimal concentration in DLS to obtain particle size distributions (PSDs) of Ti3C2 MXene nanoparticles in aqueous suspensio

Practice Profile - Piercy and Co.

Practice Name and Location: Piercy and Co, Camden, LondonPractice Website: https://www.piercyandco.com/Contribution by: Sam Twaite , Modelmaker and workshop technician Practice Statement: For us, models serve as a tool for visually and physically conveying architectural concepts. They emphasize the sculpture, materiality, and texture inherent in our design language. The most successful models we create are those that express a complex idea with clarity, and allow for a deeper understanding of the scheme's architectural approach. It's particularly valuable for us as it provides a very understandable visual language for those who are less well versed in other (2D) forms of architectural representation.This approach invites creativity and collaboration because it pulls modelmaking away from the minutia of accurate representation, and instead allows for messier, more creative models which favour concept and experimentation over meticulous accuracy. Modelmaking for us is utilised throughout the architectural process and at many different scales. In the early stages like competitions or feasibility studies, we tend to create a site model and/or larger models which express the exterior shell and main architectural moves. In the later stages we may focus on the macro and create elements which are larger scale, for example handrail details, furniture pieces, facade panels, or finishes.We also have an interiors team, so we often make models of floor plans which allow us to test interior fit-outs and furniture layouts.In-house professional modelmakers: 1Machines/equipment/workspace available for modelmaking activity.One large workshop space, divided into 3 rooms; An assembly area with 4 3D printers, laser cutting room, and a room for wood working which includes power tools like a chop saw, table saw, small band saw, sanding station and a spray booth.Materials/processes/styles used:Our main material is wood, both mdf and ply, followed by PLA (3d prints) and plaster (casting). Our models tend to be more representative and indicative rather than realistic.How modelmaking activities take place within the practice:● Architects make modelsThe practice modelmaker guides part 2 &amp; parts 1 architects through the model making process. Although he may often take the lead, it is a collaborative endeavor. Approximately half the models made at Piercy will be made by more than just one person.Indeed, my background is that I studied architecture at university and will go on to continue my studies, but for now my main focus and work is modelmaking

SEM stub preparation for freeze-cast MXene characterisation I

Freeze-cast, lyophilized and fractured Ti3C2 segments are attached to SEM stubs for morphological investigation. See attached .pdf for experimental details

XRD analysis of freeze-cast, calendered freestanding MXene film - Rigaku

An attempt to quantify variation in crystallographic texture with coupled θ:2θ scans of a freeze-cast, calendared Ti3C2 MXene film in various orientations is made. For full details of the experiment and uploaded data see the uploaded .pdf