SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

TogoID: an exploratory ID converter to bridge biological datasets

MOTIVATION

Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.

RESULTS

TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations.

AVAILABILITY AND IMPLEMENTATION

The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Development of Neonatal Airway Management Simulator for Evaluation of Tracheal Intubation

The long-term goal of this study is a training system that can simulate medical cases and advise physicians based on quantitative evaluation of neonatal resuscitation. In this paper, we designed and manufactured a neonatal airway management simulator for quantitative evaluation of tracheal intubation. This robotic simulator is equipped with 25 sensors of 6 types, which detect motions that lead to complications, inside the manikin replicated a neonate. A performance experiment of the developed sensor and an evaluation experiment with physicians were conducted. We observed that an erroneous operation in the laryngoscopy can be detected by the sensors in our simulator.

Blood coagulation status after transcatheter aortic valve implantation between the patients with vitamin k antagonist and direct oral anticoagulants

Background

Ischemic stroke after transchatheter aortic valve implantation (TAVI) was recognized. Previous study showed that the median time of a stroke was 2.0 days (IQR, 1.0–5.0) after TAVI. One of the main mechanisms for ischemic stroke after TAVI was hyper-coagulation activity associated with TAVI procedure. However, the change of coagulation status in patients with oral anticoagulant (OAC) therapy was not investigated fully.

Purpose

We investigated the difference of blood coagulation parameters between the patients with vitamin K antagonist (VKA) and those with direct oral anticoagulants (DOAC).

Methods

We enrolled 253 patients underwent transfemoral TAVI between February 2017 and March 2019 in our hospital. Of 253 patients, 71 patients (age: 85, male: 20%) took OAC therapy (VKA: 21 patients, DOAC: 50 patients). Patients who took apixaban was 32 patients, rivaroxaban was 7, edoxaban was 11. Prothrombin activation fragment 1+2 (F1+2) as a molecular marker of thrombin generation, thrombin-anti-thrombin complex (TAT) as a marker of thrombin neutralization, soluble fibrin monomer complex (SFMC) as a marker of thrombophilia and fibrin/fibrinogen degradation product (FDP) as a marker of fibrinolysis were measured before and immediately after TAVI, and on 1 and 2 day postoperatively. We also assessed ischemic stroke after TAVI between 2 groups according to BARC-2 criteria.

Results

In patients with VKA, the value of PT-INR the day before TVAI was 1.2 (1.1–1.4). The level of F1+2 in patients with VKA was significantly greater on day 0 postoperatively than those with DOAC [855 pmol/l (595–1135) vs 614 pmol/l (452–774) P=0.003]. The level of SFMC in patients with VKA was significantly greater on day 0 postoperatively than those with DOAC [37.4 μg/ml (17.3–64.5) vs. 15.7 μg/ml (8.8–27.3) P=0.002]. The level of FDP in patients with VKA was significantly greater on day 0 postoperatively than those with DOAC [VKA: 5.8 μg/ml (3.8–7.9), DOAC: 4.0 μg/ml (3.1–5.3) P=0.023]. There were no patients with ischemic stroke among 2 groups.

Conclusion

This study revealed that coagulation activity was increased after TAVI. Furthermore, the coagulation activity in patients with VKA was significantly higher than that with DOAC at especially immediately after TAVI. Careful attention should be paid to hyper-coagulation status after TAVI in patients with VKA.

Funding Acknowledgement

Type of funding source: None

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

Attenuated relationship between salivary oxytocin levels and attention to social information in adolescents and adults with autism spectrum disorder: a comparative study

BACKGROUND

Previous research studies have assessed the relationship between attention to social information and peripheral (e.g., plasma and salivary) oxytocin (OT) levels in typically developing (TD) children and children with autism spectrum disorder (ASD). A relationship between them was observed in TD children, but not in children with ASD. However, this relationship remains unexamined in other age groups. To clarify whether this lack of association is maintained throughout development in individuals with ASD, we aimed to assess the relationship between salivary OT levels and attention to social information in adolescents and adults with and without ASD.

METHODS

We recruited male adolescents and adults with ASD (n = 17) and TD participants (n = 24). Using the all-in-one eye-tracking system Gazefinder, we measured the percentage fixation time allocated to social information. We also measured the salivary OT levels and Autism Spectrum Quotient (AQ) of participants. Subsequently, we confirmed group differences and conducted a correlation analysis to investigate the relationships between these three measures.

RESULTS

Salivary OT levels did not show any significant difference between the ASD and TD groups and were negatively correlated with the AQ in the whole-group analysis, but not in within-group analysis. Individuals with ASD had significantly lower percentage fixation times than did TD individuals for eye regions in human faces with/without mouth motion, for upright biological motion, and for people regions in the people and geometry movies. The percentage of fixation for geometric shapes in the people and geometry movies was significantly higher in the ASD than in the TD group. In the TD group, salivary OT levels were positively correlated with percentage fixation times for upright biological motion and people and negatively correlated with inverted biological motion and geometry. However, no significant correlations were found in the ASD group.

CONCLUSIONS

Our exploratory results suggest that salivary OT levels in adolescents and adults with ASD are less indicative of attention to social stimuli than they are in TD adolescents and adults. It is suggested that their association is slightly weaker in adolescents and adults with ASD and that this attenuated relationship appears to be maintained throughout development.

Polarization control with an X-ray phase retarder for high-time-resolution pump-probe experiments at SACLA

Control of the polarization of an X-ray free-electron laser (XFEL) has been performed using an X-ray phase retarder (XPR) in combination with an arrival timing diagnostic on BL3 of the SPring-8 Angstrom Compact free-electron LAser (SACLA). To combine with the timing diagnostic, a pink beam was incident on the XPR crystal and then monochromated in the vicinity of samples. A high degree of circular polarization of ∼97% was obtained experimentally at 11.567 keV, which agreed with calculations based on the dynamical theory of X-ray diffraction. This system enables pump-probe experiments to be operated using circular polarization with a time resolution of 40 fs to investigate ultrafast magnetic phenomena.

TogoGenome/TogoStanza: modularized Semantic Web genome database

TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches. All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies. TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and the combinations of organisms from different taxa. The TogoGenome database exhibits a modularized structure, and each module in the report pages is separately served as TogoStanza, which is a generic framework for rendering an information block as IFRAME/Web Components, which can, unlike several other monolithic databases, also be reused to construct other databases. TogoGenome and TogoStanza have been under development since 2012 and are freely available along with their source codes on the GitHub repositories at https://github.com/togogenome/ and https://github.com/togostanza/, respectively, under the MIT license.

Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

NBDC RDF portal: a comprehensive repository for semantic data in life sciences

In the life sciences, researchers increasingly want to access multiple databases in an integrated way. However, different databases currently use different formats and vocabularies, hindering the proper integration of heterogeneous life science data. Adopting the Resource Description Framework (RDF) has the potential to address such issues by improving database interoperability, leading to advances in automatic data processing. Based on this idea, we have advised many Japanese database development groups to expose their databases in RDF. To further promote such activities, we have developed an RDF-based life science dataset repository called the National Bioscience Database Center (NBDC) RDF portal. All the datasets in this repository have been reviewed by the NBDC to ensure interoperability and queryability. As of July 2018, the service includes 21 RDF datasets, comprising over 45.5 billion triples. It provides SPARQL endpoints for all datasets, useful metadata and the ability to download RDF files. The NBDC RDF portal can be accessed at https://integbio.jp/rdf/.

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.

Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth

A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T₀)-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T₀ might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T₀. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T₀ with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV-IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.

DNA Data Bank of Japan

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.

Surface freezing and surface coverage as key factors for spontaneous formation of colloidal fibers in vacuum drying of colloidal suspensions

In this study, we investigated vacuum drying of droplets of colloidal suspension. Because of the loss of the latent heat of vaporization, the drying droplet was cooled and then formed ice. Colloidal fibers consisting of packed particles spontaneously formed when the droplet froze from the gas-liquid interface. Conversely, we observed formation of sponge-like porous structures of particles when the whole droplet almost simultaneously froze. However, the freezing mode was not the only factor for formation of colloidal fibers. We found that the surface coverage of particles on the gas-liquid interface was also important. Owing to drying, some particles accumulated at the interface before freezing. When the surface coverage was higher than a threshold value, formation of fibers was severely restricted even in the surface freezing mode. Our results clearly show the important roles of surface freezing and the surface coverage of particles on the gas-liquid interface in formation of colloidal fibers.

The health care and life sciences community profile for dataset descriptions

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

Background

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples.

Description

We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations.

Conclusions

Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

Ultrafast energy- and momentum-resolved dynamics of magnetic correlations in the photo-doped Mott insulator Sr2IrO4

Measuring how the magnetic correlations evolve in doped Mott insulators has greatly improved our understanding of the pseudogap, non-Fermi liquids and high-temperature superconductivity. Recently, photo-excitation has been used to induce similarly exotic states transiently. However, the lack of available probes of magnetic correlations in the time domain hinders our understanding of these photo-induced states and how they could be controlled. Here, we implement magnetic resonant inelastic X-ray scattering at a free-electron laser to directly determine the magnetic dynamics after photo-doping the Mott insulator Sr2IrO4. We find that the non-equilibrium state, 2 ps after the excitation, exhibits strongly suppressed long-range magnetic order, but hosts photo-carriers that induce strong, non-thermal magnetic correlations. These two-dimensional (2D) in-plane Néel correlations recover within a few picoseconds, whereas the three-dimensional (3D) long-range magnetic order restores on a fluence-dependent timescale of a few hundred picoseconds. The marked difference in these two timescales implies that the dimensionality of magnetic correlations is vital for our understanding of ultrafast magnetic dynamics.

Formation of defect-fluorite structured NdNiOxHy epitaxial thin films via a soft chemical route from NdNiO3 precursors

A new phase of oxyhydride NdNiO_xH_y with a defect-fluorite structure was obtained by a soft chemical reaction of NdNiO₃ epitaxial thin films on a substrate of SrTiO₃ (100) with CaH₂.

DNA data bank of Japan (DDBJ) progress report

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.

PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list

Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

Ultraviolet photochemical reaction of [Fe(III)(C2O4)3](3-) in aqueous solutions studied by femtosecond time-resolved X-ray absorption spectroscopy using an X-ray free electron laser

Time-resolved X-ray absorption spectroscopy was performed for aqueous ammonium iron(III) oxalate trihydrate solutions using an X-ray free electron laser and a synchronized ultraviolet laser. The spectral and time resolutions of the experiment were 1.3 eV and 200 fs, respectively. A femtosecond 268 nm pulse was employed to excite [Fe(III)(C2O4)3](3-) in solution from the high-spin ground electronic state to ligand-to-metal charge transfer state(s), and the subsequent dynamics were studied by observing the time-evolution of the X-ray absorption spectrum near the Fe K-edge. Upon 268 nm photoexcitation, the Fe K-edge underwent a red-shift by more than 4 eV within 140 fs; however, the magnitude of the redshift subsequently diminished within 3 ps. The Fe K-edge of the photoproduct remained lower in energy than that of [Fe(III)(C2O4)3](3-). The observed red-shift of the Fe K-edge and the spectral feature of the product indicate that Fe(III) is upon excitation immediately photoreduced to Fe(II), followed by ligand dissociation from Fe(II). Based on a comparison of the X-ray absorption spectra with density functional theory calculations, we propose that the dissociation proceeds in two steps, forming first [(CO2 (•))Fe(II)(C2O4)2](3-) and subsequently [Fe(II)(C2O4)2](2-).

Vacuum space charge effects in sub-picosecond soft X-ray photoemission on a molecular adsorbate layer

Vacuum space charge induced kinetic energy shifts of O 1s and Ru 3d core levels in femtosecond soft X-ray photoemission spectra (PES) have been studied at a free electron laser (FEL) for an oxygen layer on Ru(0001). We fully reproduced the measurements by simulating the in-vacuum expansion of the photoelectrons and demonstrate the space charge contribution of the high-order harmonics in the FEL beam. Employing the same analysis for 400 nm pump-X-ray probe PES, we can disentangle the delay dependent Ru 3d energy shifts into effects induced by space charge and by lattice heating from the femtosecond pump pulse.

SPARQL-enabled identifier conversion with Identifiers.org

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data.

Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data.

Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql.

Contact:sarala@ebi.ac.uk

Implementation of linked data in the life sciences at BioHackathon 2011

Background

Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data. As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data. In the process of generating RDF data, not only are data simply linked to one another, the links themselves are characterized by ontologies, thereby allowing the types of links to be distinguished. Although there is a high labor cost to define an ontology for data providers, the merit lies in the higher level of interoperability with data analysis and visualization software. This increase in interoperability facilitates the multi-faceted retrieval of data, and the appropriate data can be quickly extracted and visualized. Such retrieval is usually performed using the SPARQL (SPARQL Protocol and RDF Query Language) query language, which is used to query RDF data stores. For the database provider, such interoperability will surely lead to an increase in the number of users.

Results

This manuscript describes the experiences and discussions shared among participants of the week-long BioHackathon 2011 who went through the development of RDF representations of their own data and developed specific RDF and SPARQL use cases. Advice regarding considerations to take when developing RDF representations of their data are provided for bioinformaticians considering making data available and interoperable.

Conclusions

Participants of the BioHackathon 2011 were able to produce RDF representations of their data and gain a better understanding of the requirements for producing such data in a period of just five days. We summarize the work accomplished with the hope that it will be useful for researchers involved in developing laboratory databases or data analysis, and those who are considering such technologies as RDF and Linked Data.

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. Since October 2013, DDBJ Center has operated the Japanese Genotype-phenotype Archive (JGA) in collaboration with our partner institute, the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency. DDBJ Center provides the JGA database system which securely stores genotype and phenotype data collected from individuals whose consent agreements authorize data release only for specific research use. NBDC has established guidelines and policies for sharing human-derived data and reviews data submission and usage requests from researchers. In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science. This paper describes the overview of the JGA project, updates to the DDBJ databases, and services for data retrieval, analysis and integration.

High-precision x-ray FEL pulse arrival time measurements at SACLA by a THz streak camera with Xe clusters

The accurate measurement of the arrival time of a hard X-ray free electron laser (FEL) pulse with respect to a laser is of utmost importance for pump-probe experiments proposed or carried out at FEL facilities around the world. This manuscript presents the latest device to meet this challenge, a THz streak camera using Xe gas clusters, capable of pulse arrival time measurements with an estimated accuracy of several femtoseconds. An experiment performed at SACLA demonstrates the performance of the device at photon energies between 5 and 10 keV with variable photon beam parameters.

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Background

Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches.

Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large.

Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together.

Results

This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities.

Conclusions

Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum

To understand the molecular mechanisms of parasitism in vivo, it is essential to elucidate how the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped the RNA-seq tags to the human and Pf reference genomes to separate the respective tags. We were thus able to simultaneously analyze expression patterns in both humans and parasites. We identified human and parasite genes and pathways that correlated with various clinical data, which may serve as primary targets for drug developments. Of particular importance, we revealed characteristic expression changes in the human innate immune response pathway genes including TLR2 and TICAM2 that correlated with the severity of the malaria infection. We also found a group of transcription regulatory factors, JUND, for example, and signaling molecules, TNFAIP3, for example, that were strongly correlated in the expression patterns of humans and parasites. We also identified several genetic variations in important anti-malaria drug resistance-related genes. Furthermore, we identified the genetic variations which are potentially associated with severe malaria symptoms both in humans and parasites. The newly generated data should collectively lay a unique foundation for understanding variable behaviors of the field malaria parasites, which are far more complex than those observed under laboratory conditions.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output.