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265 results for “developer tools”
Developers eXperience (DX) in ALM software tools: an investigation on virtual kanban boards
<p>Video de backup da apresentação do artigo "Developers eXperience (DX) in ALM software tools: an investigation on virtual kanban boards" no SBES 2020 - Trilha de Ideias Inovadoras e Resultados Emergentes. </p>
Data from: Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool
<p>Significant declines in Atlantic sturgeon (<i>Acipenser oxyrhynchus oxyrhynchus</i>) abundances along the US east coast have spurred major research efforts and management actions over the last 50 years, yet information on spawning stock abundances and habitat use is still lacking for many river systems, including in the Chesapeake Bay, USA. Here, we developed and tested a new quantitative PCR (qPCR) assay to detect Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal of providing an alternative method to monitor presence and relative abundance. We also examined Atlantic sturgeon eDNA shedding rates in laboratory experiments. A qPCR-probe assay targeting Cytochrome-B was developed and showed no amplification of other related and co-occurring fishes. Pond trials at a density of ~0.2 g/L sturgeon produced relatively strong eDNA detections (~1,000-25,000 copies/L) in all seven water samples assayed. Water samples taken from two river systems in the Chesapeake Bay produced zero eDNA detections in the summer, while fall sampling during sturgeon spawning produced positive eDNA detections in 26% of samples, though at much lower concentrations (400-1,800 copies/L) compared with the pond (mesocosm) detections. Acoustic detections of sturgeon near river sampling sites were positively associated with eDNA detections. However, the eDNA assay failed to detect the presence of sturgeon in some samples when abundances were very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that relatively weak detections in the field are not necessarily driven by low rates of eDNA shedding. Overall, eDNA analysis represents a promising new monitoring tool for Atlantic sturgeon. Applying these methods in other rivers along the US east coast is an important next step in documenting Atlantic sturgeon distribution for management and conservation purposes.</p>
Data from: Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus
The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Data from: Development of a simple, practice-based tool to assess quality of paediatric emergency care delivery in resource-limited settings: identifying critical actions via a Delphi study
Objective: Provision of timely, high-quality care for the initial management of critically ill children in African hospitals remains a challenge. Monitoring the completion of critical actions during resuscitations can inform efforts to reduce variability and improve outcomes. We sought to develop a practice-based tool based on contextually relevant actions identified via a Delphi process. Our goal was to develop a tool that could identify gaps in care, facilitate identification of training and standardized assessment to support quality improvement efforts. Design: Six sentinel conditions were selected based on disease epidemiology and mortality at rural and urban African emergency departments. Potential critical actions were identified through focused literature review. These actions were evaluated within a three-round modified Delphi process. A set of logistical filters was applied to the candidate list to derive a practice-based tool. Setting and participants: Attendees at an international emergency medicine conference comprised an expert panel of 25 participants, with 84% working primarily in African settings. Consensus rounds allowing novel responses were conducted via online and in-person surveys. Results: The expert panel generated 199 actions that apply to six conditions in emergently ill children. Application of appropriateness criteria refined this to 92 candidate actions across seven categories: core skills, active seizure, altered mental status, diarrheal illness, febrile illness, respiratory distress, polytrauma. From these, we identified 28 actions for inclusion in a practice-based tool contextually relevant to the initial management of critically ill children in Africa. Conclusions: A group consensus process identified critical actions for severely ill children with select sentinel conditions in emergency paediatric care in an African setting. Absence of these actions during resuscitation might reflect modifiable gaps in quality of care. The resulting practice-based tool is context-relevant and can serve as a foundation for training and quality improvement efforts in African hospitals and emergency departments.
Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases the matching Genbank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
Data from: Where to start? development of a spatial tool to prioritise retrofitting of power line poles that are dangerous to raptors
1.Avian electrocution on power lines is a major conservation issue on a global scale. Electrocution risk models have recently been proposed as an effective alternative to prioritising high‐risk pole retrofitting activities at a large scale. However, existing models ignore the specific features of the power poles supporting the power distribution lines and make the tenuous assumption that pole density and power line length are key factors to assessing the electrocution risk at a large scale. This assumption may be violated in areas with high variations in pole configuration. 2.In this study, we used data on raptors electrocuted on poles to develop a predictive model of raptor electrocution risk throughout an extensive geographic area in north‐western Spain, using boosted regression trees (BRT). With the best‐fitting model we predicted the hazard of a set of 188 741 poles and validated the model predictions with new data collected from the study area. 3.Our model highlights the relevance of combining both habitat and technical features to identify the most dangerous poles for raptors on a large geographic scale. A 9·86% of the total poles evaluated were characterised as high risk for raptors. The model showed good performance in external validation. The new electrocution events were registered at poles with high‐risk values. 4.Synthesis and applications. In this study we improved the accuracy of the predictive models of raptor electrocution risk for large geographic areas. By incorporating the technical characteristics of the power poles into the models, we achieved a high level of prediction at the power pole level which is the ultimate correction unit. This will allow electric companies and wildlife managers to specify retrofitting activities of high‐risk power poles for raptors in large geographic areas, thus maximizing the effect of investment in the correction of dangerous power poles and conservation of the raptor populations.
Dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"
<p>Raw dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"</p>
Fig. 1 a –d Marine benthic organisms used for bio-optical measurements. a Boneccia viridis, b Isodictya pacmata, c Hymedesmia paupertas, d in Development of hyperspectral imaging as a bio-optical taxonomic tool for pigmented marine organisms
Fig. 1 a –d Marine benthic organisms used for bio-optical measurements. a Boneccia viridis, b Isodictya pacmata, c Hymedesmia paupertas, d Hymedesmia sp.
Data from: Developing state and transition models of floodplain vegetation dynamics as a tool for conservation decision-making: a case study of the Macquarie Marshes Ramsar wetland
1. Floodplain vegetation states (communities) exhibit spatiotemporal dynamics in vegetation structure and composition, which reflect unique hydrological and connectivity patterns. Shifts in inundation regimes can drive succession and establish new stable states, determined by the magnitude and duration of the hydrological perturbation. 2. We aimed to develop a modelling approach that is able to capture ecosystem dynamics, identify and quantify the main drivers of change, and provide a tool for conservation decision-making. We developed state and transition models for floodplain vegetation states based on surveys in 1991 and 2008 in the Macquarie Marshes (Australia), a Ramsar wetland of international importance. We used a Bayesian logistic regression approach to model state and transitions between vegetation states and investigated how flood frequency, distance to stream and fire frequency were associated with vegetation dynamics during this period. 3. During 1991–2008, significant transitions have occurred towards drier states. Semi-permanent wetland vegetation had the lowest persistence probability (ppsis = 0·456) and a significant threshold response of transitioning to terrestrial vegetation (ptran = 0·505). Transition to drier states was driven by lower inundation probabilities followed by increased fire probability, and distance to nearest stream. 4. Using developed models, we predicted persistence probabilities of vegetation states under an unregulated (i.e. no dams or diversions) and regulated water availability system. Under a regulated system, semi-permanent wetland vegetation had an average persistence of ppsis = 0. 67 and 0·08 in the northern and southern sections of the nature reserve, respectively. Under an unregulated system, the predicted persistence of semi-permanent wetland vegetation was considerably higher: ppsis = 0·87 and 0·38, respectively. 5. Synthesis and applications. Developing quantitative models of state transitions significantly improved our understanding of ecosystem dynamics, identifying sensitive indicators for monitoring and thus supporting conservation decision-making. This helps managers understand potential trajectories of change in ecosystems in response to management options. For example, increasing environmental flows in the Macquarie Marshes is predicted to shift the community towards more of a wetland than the terrestrial state, resulting from river regulation. State and transition models identified how key ecological assets respond to drivers of change, particularly where these can be managed. This is critical for ensuring that all ecosystem components are managed and that these do not shift into undesirable states.
FIGURE 3 in ZooBank: Developing a nomenclatural tool for unifying 250 years of biological information*
FIGURE 3. Components of an LSID. There does not appear to be a consistent implementation of the version part of the LSID, and it is not incorporated into ZooBank LSIDs.
Open source and open hardware: developing tools that are accessible and customisable
<p><strong>The following video describes how ROMI uses open source hardware to support communities through customisation and adaptation. Funded by EU Grant 773875.</strong></p> <p><em>Videos are available in:</em></p> <ul> <li>Hi-res (1080p Apple ProRes)</li> <li>Mid-res (1080p H265)</li> </ul> <p><strong>Video script:</strong></p> <p>(MINCHIN) A key aspect and component of the ROMI project is that it should be open source so there is no proprietary software there's no ownership over the designs in fact it's created to be hacked customised and adapted to any farm.<br> <br> (HANAPPE) One of the aspects of the ROMI project is open hardware and we started from scratch like buying a motor buying a motor-controller programming the motor controller and which is maybe different than many of the projects you might see more industrial projects who might rely more on say high-end standard components from from the industry but i think there's a real advantage in trying to build everything up is that first you understand everything you can explain everything you can fix anything you can you know document anything for you know DIY farmers that they you know if they want to replace one motor with another and understanding that all allows you to quickly experiment stuff without having to depend on someone else who's working with say a closed source component and it allows you to be quite reactive and of course in the end allows you to be fairly cost effective.<br> <br> (BAORI) One of the things we set out to do with this project was to make it accessible and the idea is that at the end of the project everything will be open source so from the frame to the software the designs the cad everything will be open source so if you're a maker if you're somebody who is an engineer and wants to build one of these robots yourself you'll be able to download everything including the software to be able to make it run and because we wanted it to be accessible we started out with one thought that was everything that we put into this rover should also be accessible.<br> <br> (CAMPRODON) So we are trying to bring that philosophy that is embedded within Fab Labs slash (/) maker movement at large the open hardware movement, of how you design for distributed manufacturing. Which means that you take design decisions on the way that you build things which are meant for others replicated in new laboratories using new machines and you do that on top of a network such as a Fab Lab network which is a robust yet heterogeneous.<br> <br> (BARBERAN) It seems like someone tinkered with it. The idea when we design this is to constrain ourselves to do it in a way that anyone else can build it easily. So we try to keep the type and the complexity of the tools we use as small and simple as we can, so we use 3d printers that today are really accessible, we use CNC machines that's maybe the the most complex machine we use but it was it was needed because we need to build something that can stand the weather in a harsh environment in a farm. So we use aluminium and plastic and the rest of the components are mostly commercial components so the the process of designing it is a common go between the computer and the farm and the fab lab we tried here with the cable on the office to hang the first versions of the of the cable bot then we come back to redesign the pieces and then we adjust the sizes of the pulleys and the springs and then we do another model. And so this ability to reiterate so fast is also provided by the simplicity of the tools we use. Using a really simple 3d printer to build a robot is allows you to do in one month several versions and iterations of the same robot.<br> <br> (HANAPPE) In the end our goal is sustainability it's not technology, and what is the best way for whatever we build to have an impact on on say farmers in Europe or wider, and if if what we do is good then we would like them to have access to these tools, and there's some sort of a confidence that then there will be some financing flowing back to us.<br> <br> (MINCHIN) When we open source this knowledge and these tools it allows for an abundance of researchers of practitioners to come together to find the solutions, we don't have to depend on a small development team so the the library of tools that are developed are really a public library for others to to use and to adapt.<br> <br> (BARBERAN) At the end I think the the most important part that we don't even realise because we just do it because we are on the on the inertia of doing it is that we are setting rocks for the future. At the end we are not making right now the the the best robot the best tool what we are doing is setting ground to build on the future the best robot and the best thing built by people not by us because we don't we are not farmers we are not going to design the best robot and we are not a big company with resources as crazy to to make the ultra high-tech thing. But we are able to do something to share with people and a lot of heads think better than a couple of heads you know. The the model that that linux a lot of people in the linux community use is we are dumber than them but we are hundreds of thousands. Hundreds of thousands of heads think better than 10 heads so being able to share that knowledge and to include people in in the development of their own tools i think is the best part on a mid and long term way of seeing this.</p>
Software tools used in ROMI: a quick look into some of the tools used to develop ROMI
<p><strong>The following video describes ROMI's principles and methods for designing with free and open source software and hardware. Funded by EU Grant 773875.</strong></p> <p><em>Videos are available in:</em></p> <ul> <li>Hi-res (1080p Apple ProRes)</li> <li>Mid-res (1080p H265)</li> </ul> <p><strong>Video script:</strong></p> <p>(BARBERAN) ROMI develops open tools for farming communities. But I prefer not to say open tools I prefer to say ‘free’ tools. Free not as in ‘Gratis’, not as in it doesn't have a cost, but as in ‘freedom’ you know because it's not the same. And and I think we all in ROMI project agree that we are more in the side of ‘free’ as in ‘freedom’ than in ‘open’ as in you can see what I do. It's more that I can do this, and you can use it for whatever you want and modify it as you want.<br> <br> Hi, I'm Victor, I'm an industrial designer here at the Fab LaN in Barcelona, and I work mostly work developing hardware and software. So the idea is that using free tools gives you control of what you do, so we try to do all the chain, all the the flow with with open source tools, with free tools. So we use Linux that's a free operative system, that anyone can download and use on their own computers. It's installable in any type of computer in any type of TV, in most watches. Super computers use Linux all over the world on top of Linux we use different tools to do the different tasks. We use ‘Blender’ for example for modelling Blender is a tool that can do a lot of tough animation 3D modelling, 3D sculpting Etc. And here we use it like for a strange thing like designing robots, but it's a really nice tool for even design stuff like this, the cabling then all the mechanical parts etc.<br> <br> Then for doing the in fact the electronic boards we use a ‘kiCAD’ that's a really nice software to design electronic boards we do all the electronic design here and we produce the boards later. We try to keep it in a way that boards can be produced locally but not always easy depending on the type of task that you want to do.<br> <br> We're using ‘Inscape’ like a normal open source and free drawing program that anyone can use. And we replace tools that cost a lot of money, and that you cannot customise to do whatever you want. For a coding we try to also keep using only three tools. So it depends on on it's a personal choice, I use ‘VIM’. We use all the the libraries developed by the Arduino project, that's a free really important free software project. We use platform IO, another set of tools to organise libraries to set up stuff to compile, to upload code to different processors.<br> <br> We use a lot of libraries developed by a lot of people all over the world with different interests. Libraries to control motors, libraries to read sensors, libraries to do whatever kind of things people have faced in their own tasks. The people write the library and share it so we got it, and if we see some problems we improve it, or we change it, and we re-share it again. So people can reuse whatever we are doing you know at the end this kind of projects are public money, and there's one model that's being promoted that is; ‘public money, public code’. You know, so it's a more or less the idea that we try to push.<br> <br> Everything I just showed to you in my computer, you can install it in yours because it's free and you can download all the models and all the code and modify it by yourself to build your own robots, and customise them to your own use. All the process that we do it's important, because at the end there's a lot of knowledge being generated we tested a lot of different motors with a lot of different open source and free controllers, and we document all the process so people can get advantage of that work. Here for example so we we use a remote controller and we try different remote controllers and we test the stability Etc and we document all the tests that we do and how we solve the problem in terms of code in terms of electronics in terms of algorithms etc. In since we are adapting for example we are adapting a mouse sensor to measure the position on top of the cable, then we do a lot of experimentation and if we document that experiment people can get advantage of it. Not of the final product but of the process that we did. Because people learn how to use that Mouse sensors to do different stuff.</p>
Data underlying the publication Development and implementation of a risk assessment tool for broiler farm biosecurity and a health intervention plan in the Netherlands, Greece, and Cyprus
<p>Introduction</p> <p>Preventing pathogens from entering and spreading on farms is the first step in reducing health problems.<br> For this study a BiosEcurity Assessment Tool was developed to identify strengths and weaknesses in biosecurity on broiler farms,<br> which was used as a starting point to formulate tailor-made health plans to improve broiler health and reduce antimicrobial use.</p> <p>Measurements and data collection</p> <p>Farms were divided into 3 separate areas according to associated biosecurity risk; high disease risk external areas (red zone), medium risk service areas (orange zone),<br> and the clean and highly secure access-restricted green zone. In the Netherlands, Cyprus, and Greece, 13, 15, and 7 broiler houses were monitored for 4 production cycles (2 preintervention and 2 postintervention cycles).<br> At the start of the study the BiosEcurity Assessment Tool assessment was performed and a health plan was made in consultation with the veterinarian.<br> After the second cycle a start was made with the implementation of the health plan.</p>
Developing a Pipeline to Employ RNA-Seq as a Complementary Diagnostic Tool in Rare Diseases
ClinicalTrials.gov study NCT05996731. IPD Sharing: NO. Countries: 1. Publications: 3.
Development of a Novel Risk Prediction Tool for Emergency Department Patients Symptoms of Coronary Artery Disease
ClinicalTrials.gov study NCT06743672. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Developing Field Tools for Real-Time Assessment of Exposure to Psychosocial Stress and Drug Use in an Outpatient Treatment Population
ClinicalTrials.gov study NCT00787423. IPD Sharing: NO. Countries: 1. Publications: 1.
Development of a Self-administered Neck Mobility Assessment Tool in Chronic Neck Pain Patients.
ClinicalTrials.gov study NCT02754934. IPD Sharing: NO. Countries: 1. Publications: 1.
Development of Tools for Respiration and Circulation Exploration
ClinicalTrials.gov study NCT02114749. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Development of Quality of Life Tool for TBI
ClinicalTrials.gov study NCT00714428. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.