BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively.
Ontology highlight
ABSTRACT:
SUBMITTER: Li K
PROVIDER: S-EPMC8766334 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Given an mRNA sequence as input, the OligoWalk web server generates a list of small interfering RNA (siRNA) candidate sequences, ranked by the probability of being efficient siRNA (silencing efficacy greater than 70%). To accomplish this, the server predicts the free energy changes of the hybridization of an siRNA to a target mRNA, considering both siRNA and mRNA self-structure. The free energy changes of the structures are rigorously calculated using a partition function calculation. By changing advanced options, the free energy changes can also be calculated using less rigorous lowest free energy structure or suboptimal structure prediction methods for the purpose of comparison. Considering the predicted free energy changes and local siRNA sequence features, the server selects efficient siRNA with high accuracy using a support vector machine. On average, the fraction of efficient siRNAs selected by the server that will be efficient at silencing is 78.6%. The OligoWalk web server is freely accessible through internet at http://rna.urmc.rochester.edu/servers/oligowalk.
| S-EPMC2447759 | biostudies-literature
Project description:This study investigates the effectiveness of the online Flash game Disease Defenders in producing knowledge gains for concepts related to the scientific process. Disease Defenders was specifically designed to model how the scientific process is central to a variety of disciplines and science careers. An additional question relates to the game's ability to shift attitudes toward science. Middle school classes from grades six to eight were assigned to the experimental group (n = 489) or control group (n = 367) and asked to participate in a three-session intervention. The sessions involved completing a pretest, a game play session, and taking a posttest. Students in the experimental group played Disease Defenders while students in the control group played an alternative science game. Results showed a significant increase in mean science knowledge scores for all grades in the experimental group, with sixth grade and seventh grade students gaining more knowledge than eighth grade students. Additionally, results showed a significant positive change in science attitudes only among sixth graders, who also rated their satisfaction with the game more favorably than students in higher grades. No differences in mean test scores were found between genders for science knowledge or science attitudes, suggesting that the game is equally effective for males and females.
| S-EPMC3706166 | biostudies-literature
Project description:Objectives:Patients have unique information needs to help them interpret and make decisions about laboratory test results they receive on web-based portals. However, current portals are not designed in a patient-centered way and little is known on how best to harness patients' information needs to inform user-centered interface design of portals. We designed a patient-facing laboratory test result interface prototype based on requirement elicitation research and used a mixed-methods approach to evaluate this interface. Methods:After designing an initial test result display prototype, we used multiple evaluation methods, including focus group review sessions, expert consultation, and user testing, to make iterative design changes. For the user testing component, we recruited 14 patient-users to collect and analyze three types of data: comments made during testing sessions, responses to post-session questionnaires, and system usability scores. Results:Our initial patient-centered interface design included visual ranges of laboratory values, nontechnical descriptions of the test and result, and access to features to help patients interpret and make decisions about their results. Findings from our evaluation resulted in 6 design iterations of the interface. Results from user testing indicate that the later versions of the interface fulfilled patient's information needs, were perceived as usable, and provided access to information and techniques that facilitated patient's ability to derive meaning from each test result. Conclusions:Requirement elicitation studies can inform the design of a patient-facing test result interface, but considerable user-centered design efforts are necessary to create an interface that patients find useful. To promote patient engagement, health information technology designers and developers can use similar approaches to enhance user-centered software design in patient portals.
| S-EPMC6078112 | biostudies-literature
Project description:In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.
| S-EPMC5604942 | biostudies-literature
Project description:This paper presents the design and evaluation of a new controller for a multi-finger tactual display in speech communication. A two-degree-of-freedom controller consisting of a feedback controller and a prefilter and its application in a consonant contrasting experiment are presented. The feedback controller provides stable, fast, and robust response of the fingerpad interface and the prefilter shapes the frequency-response of the closed-loop system to match with the human detection-threshold function. The controller is subsequently used in a speech communication system that extracts spectral features from recorded speech signals and presents them as vibrational-motional waveforms to three digits on a receiver's left hand. Performance from a consonantal contrast test suggests that participants are able to identify tactual cues necessary for discriminating consonants in the initial position of consonant-vowel-consonant (CVC) segments. The average sensitivity indices for contrasting voicing, place, and manner features are 3.5, 2.7, and 3.4, respectively. The results show that the consonantal features can be successfully transmitted by utilizing a broad range of the kinesthetic-cutaneous sensory system. The present study also demonstrates the validity of designing controllers that take into account not only the electromechanical properties of the hardware, but the sensory characteristics of the human user.
| S-EPMC2736701 | biostudies-other
Project description:Investigation of physiological mechanisms at a cellular level often requires production of high-quality antibodies, frequently using synthetic peptides as immunogens. Here we describe a new, web-based software tool called NHLBI-AbDesigner that allows the user to visualize the information needed to choose optimal peptide sequences for peptide-directed antibody production (http://helixweb.nih.gov/AbDesigner/). The choice of an immunizing peptide is generally based on a need to optimize immunogenicity, antibody specificity, multispecies conservation, and robustness in the face of posttranslational modifications (PTMs). AbDesigner displays information relevant to these criteria as follows: 1) "Immunogenicity Score," based on hydropathy and secondary structure prediction; 2) "Uniqueness Score," a predictor of specificity of an antibody against all proteins expressed in the same species; 3) "Conservation Score," a predictor of ability of the antibody to recognize orthologs in other animal species; and 4) "Protein Features" that show structural domains, variable regions, and annotated PTMs that may affect antibody performance. AbDesigner displays the information online in an interactive graphical user interface, which allows the user to recognize the trade-offs that exist for alternative synthetic peptide choices and to choose the one that is best for a proposed application. Several examples of the use of AbDesigner for the display of such trade-offs are presented, including production of a new antibody to Slc9a3. We also used the program in large-scale mode to create a database listing the 15-amino acid peptides with the highest Immunogenicity Scores for all known proteins in five animal species, one plant species (Arabidopsis thaliana), and Saccharomyces cerevisiae.
| S-EPMC3328907 | biostudies-literature
Project description:The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects.
| S-EPMC5106875 | biostudies-literature
Project description:Since its discovery almost 70 years ago, the hologram has been considered to reproduce the most realistic three dimensional images without visual side effects. Holographic video has been extensively researched for commercialization, since Benton et al. at MIT Media Lab developed the first holographic video systems in 1990. However, commercially available holographic video displays have not been introduced yet for several reasons: narrow viewing angle, bulky optics and heavy computing power. Here we present an interactive slim-panel holographic video display using a steering-backlight unit and a holographic video processor to solve the above issues. The steering-backlight unit enables to expand the viewing angle by 30 times and its diffractive waveguide architecture makes a slim display form-factor. The holographic video processor computes high quality holograms in real-time on a single-chip. We suggest that the slim-panel holographic display can provide realistic three-dimensional video in office and household environments.
| S-EPMC7655945 | biostudies-literature
Project description:The ever-increasing quantity and complexity of scientific production have made it difficult for researchers to keep track of advances in their own fields. This, together with growing popularity of online scientific communities, calls for the development of effective information filtering tools. We propose here an algorithm which simultaneously computes reputation of users and fitness of papers in a bipartite network representing an online scientific community. Evaluation on artificially-generated data and real data from the Econophysics Forum is used to determine the method's best-performing variants. We show that when the input data is extended to a multilayer network including users, papers and authors and the algorithm is correspondingly modified, the resulting performance improves on multiple levels. In particular, top papers have higher citation count and top authors have higher h-index than top papers and top authors chosen by other algorithms. We finally show that our algorithm is robust against persistent authors (spammers) which makes the method readily applicable to the existing online scientific communities.
| S-EPMC4251832 | biostudies-literature
Project description:One of the primary aims of synthetic biology is to (re)design metabolic pathways towards the production of desired chemicals. The fast pace of developments in molecular biology increasingly makes it possible to experimentally redesign existing pathways and implement de novo ones in microbes or using in vitro platforms. For such experimental studies, the bottleneck is shifting from implementation of pathways towards their initial design. Here, we present an online tool called 'Metabolic Tinker', which aims to guide the design of synthetic metabolic pathways between any two desired compounds. Given two user-defined 'target' and 'source' compounds, Metabolic Tinker searches for thermodynamically feasible paths in the entire known metabolic universe using a tailored heuristic search strategy. Compared with similar graph-based search tools, Metabolic Tinker returns a larger number of possible paths owing to its broad search base and fast heuristic, and provides for the first time thermodynamic feasibility information for the discovered paths. Metabolic Tinker is available as a web service at http://osslab.ex.ac.uk/tinker.aspx. The same website also provides the source code for Metabolic Tinker, allowing it to be developed further or run on personal machines for specific applications.
| S-EPMC3675468 | biostudies-literature