Viruses, Immunology & Bioinformatics from Virology.uvic.ca
97.1K views | +36 today
Follow
 
Scooped by Chris Upton + helpers
onto Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Scoop.it!

The Hitchhiker’s Guide to Python! — The Hitchhiker's Guide to Python

The Hitchhiker’s Guide to Python! — The Hitchhiker's Guide to Python | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

This opinionated guide exists to provide both novice and expert Python developers a best-practice handbook to the installation, configuration, and usage of Python on a daily basis.

more...
No comment yet.
Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

more...
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
Rescooped by Chris Upton + helpers from plant microbe interaction genomics
Scoop.it!

Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics

Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Background
Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.

Results
Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Conclusions
Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.


Via Ronny Kellner, Matt Agler, Jessie Uehling
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Hazard Characterization of Modified Vaccinia Virus Ankara Vector: What Are the Knowledge Gaps?

Hazard Characterization of Modified Vaccinia Virus Ankara Vector: What Are the Knowledge Gaps? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Modified vaccinia virus Ankara (MVA) is the vector of choice for human and veterinary applications due to its strong safety profile and immunogenicity in vivo. The use of MVA and MVA-vectored vaccines against human and animal diseases must comply with regulatory requirements as they pertain to environmental risk assessment, particularly the characterization of potential adverse effects to humans, animals and the environment. MVA and recombinant MVA are widely believed to pose low or negligible risk to ecosystem health. However, key aspects of MVA biology require further research in order to provide data needed to evaluate the potential risks that may occur due to the use of MVA and MVA-vectored vaccines. The purpose of this paper is to identify knowledge gaps in the biology of MVA and recombinant MVA that are of relevance to its hazard characterization and discuss ongoing and future experiments aimed at providing data necessary to fill in the knowledge gaps. In addition, we presented arguments for the inclusion of uncertainty analysis and experimental investigation of verifiable worst-case scenarios in the environmental risk assessment of MVA and recombinant MVA. These will contribute to improved risk assessment of MVA and recombinant MVA vaccines.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Begomoviral Movement Protein Effects in Human and Plant Cells: Towards New Potential Interaction Partners

Begomoviral Movement Protein Effects in Human and Plant Cells: Towards New Potential Interaction Partners | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Geminiviral single-stranded circular DNA genomes replicate in nuclei so that the progeny DNA has to cross both the nuclear envelope and the plasmodesmata for systemic spread within plant tissues. For intra- and intercellular transport, two proteins are required: a nuclear shuttle protein (NSP) and a movement protein (MP). New characteristics of ectopically produced Abutilon mosaic virus (AbMV) MP (MPAbMV), either authentically expressed or fused to a yellow fluorescent protein or epitope tags, respectively, were determined by localization studies in mammalian cell lines in comparison to plant cells. Wild-type MPAbMV and the distinct MPAbMV: reporter protein fusions appeared as curled threads throughout mammalian cells. Co-staining with cytoskeleton markers for actin, intermediate filaments, or microtubules identified these threads as re-organized microtubules. These were, however, not stabilized by the viral MP, as demonstrated by nocodazole treatment. The MP of a related bipartite New World begomovirus, Cleome leaf crumple virus (ClLCrV), resulted in the same intensified microtubule bundling, whereas that of a nanovirus did not. The C-terminal section of MPAbMV, i.e., the protein’s oligomerization domain, was dispensable for the effect. However, MP expression in plant cells did not affect the microtubules network. Since plant epidermal cells are quiescent whilst mammalian cells are proliferating, the replication-associated protein RepAbMV protein was then co-expressed with MPAbMV to induce cell progression into S-phase, thereby inducing distinct microtubule bundling without MP recruitment to the newly formed threads. Co-immunoprecipitation of MPAbMV in the presence of RepAbMV, followed by mass spectrometry identified potential novel MPAbMV-host interaction partners: the peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Pin4) and stomatal cytokinesis defective 2 (SCD2) proteins. Possible roles of these putative interaction partners in the begomoviral life cycle and cytoskeletal association modes are discussed.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the “Hard Fruit Syndrome” of Watermelon

Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the “Hard Fruit Syndrome” of Watermelon | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Chickpea chlorotic dwarf virus (CpCDV), a polyphagous mastrevirus, family Geminiviridae, has been recently linked to the onset of the “hard fruit syndrome” of watermelon, first described in Tunisia, that makes fruits unmarketable due to the presence of white hard portions in the flesh, chlorotic mottling on the rind, and an unpleasant taste. To investigate the etiological agent of this disease, total RNA extracted from symptomatic watermelon fruits was subjected to small RNA sequencing through next generation sequencing (NGS) techniques. Data obtained showed the presence of CpCDV and two other viral species. However, following validation through polymerase chain reaction (PCR), CpCDV was the only viral species consistently detected in all samples. Watermelon seedlings were then challenged by an agroinfectious CpCDV clone; several plants proved to be CpCDV-infected, and were able to produce fruits. CpCDV infected and replicated in watermelon fruits and leaves, leading to abnormality in fruits and in seed production, similar to those described in field. These results indicate that CpCDV is the etiological agent of the “hard fruit syndrome” of watermelon.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

How a quarter of the cow genome came from snakes

How a quarter of the cow genome came from snakes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome is made up of bits of DNA that hav…
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus

Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Feasibility and Acceptability of HPV Self-Collection Cervical Cancer Screening and Treatment in Botswana

Feasibility and Acceptability of HPV Self-Collection Cervical Cancer Screening and Treatment in Botswana | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Clinical Trials - clinicaltrials.gov Aims of the Study: To assess feasibility and acceptability of introducing HPV testing of self-collected vaginal specimen
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

A Method for the Acute and Rapid Degradation of Endogenous Proteins

A Method for the Acute and Rapid Degradation of Endogenous Proteins | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Methods for the targeted disruption of protein function have revolutionized science and greatly expedited the systematic characterization of genes. Two main approaches are currently used to disrupt protein function: DNA knockout and RNA interference, which act at the genome and mRNA level, respectively. A method that directly alters endogenous protein levels is currently not available. Here, we present Trim-Away, a technique to degrade endogenous proteins acutely in mammalian cells without prior modification of the genome or mRNA. Trim-Away harnesses the cellular protein degradation machinery to remove unmodified native proteins within minutes of application. This rapidity minimizes the risk that phenotypes are compensated and that secondary, non-specific defects accumulate over time. Because Trim-Away utilizes antibodies, it can be applied to a wide range of target proteins using off-the-shelf reagents. Trim-Away allows the study of protein function in diverse cell types, including non-dividing primary cells where genome- and RNA-targeting methods are limited.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Reference-guided de novo assembly approach improves genome reconstruction for related species

Reference-guided de novo assembly approach improves genome reconstruction for related species | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.
more...
No comment yet.
Rescooped by Kenzibit from Virology News
Scoop.it!

Namibia Gets Over U.S. $30 Million War Chest to Fight HIV

Namibia Gets Over U.S. $30 Million War Chest to Fight HIV | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Namibia has signed an amendment to the 2007 bilateral grant agreement with the USA to add N$435 million of funding under the US government's President's Emergency Plan for AIDS Relief (PEPFAR), to help fight against the HIV/AIDS pandemic.

Via Ed Rybicki
more...
No comment yet.
Rescooped by Chris Upton + helpers from Aquatic Viruses
Scoop.it!

The enigmatic archaeal virosphere

The enigmatic archaeal virosphere | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus–host interactions, including interactions with archaeal CRISPR–Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.


Via Ed Rybicki
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly

Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The orthopoxviruses (OPV) comprise several emerging viruses with great importance to human and veterinary medicine, including vaccinia virus (VACV), which causes outbreaks of bovine vaccinia (BV) in South America. Historically, VACV is the most comprehensively studied virus, however, its origin and natural hosts remain unknown. VACV was the primary component of the smallpox vaccine, largely used during the smallpox eradication campaign. After smallpox was declared eradicated, the vaccination that conferred immunity to OPV was discontinued, favoring a new contingent of susceptible individuals to OPV. VACV infections occur naturally after direct contact with infected dairy cattle, in recently vaccinated individuals, or through alternative routes of exposure. In Brazil, VACV outbreaks are frequently reported in rural areas, affecting mainly farm animals and humans. Recent studies have shown the role of wildlife in the VACV transmission chain, exploring the role of wild rodents as reservoirs that facilitate VACV spread throughout rural areas. Furthermore, VACV circulation in urban environments and the significance of this with respect to public health, have also been explored. In this review, we discuss the history, epidemiological, ecological and clinical aspects of natural VACV infections in Brazil, also highlighting alternative routes of VACV transmission, the factors involved in susceptibility to infection, and the natural history of the disease in humans and animals, and the potential for dissemination to urban environments.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Structures and Functions of the Envelope Glycoprotein in Flavivirus Infections

Structures and Functions of the Envelope Glycoprotein in Flavivirus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Flaviviruses are enveloped, single-stranded RNA viruses that widely infect many animal species. The envelope protein, a structural protein of flavivirus, plays an important role in host cell viral infections. It is composed of three separate structural envelope domains I, II, and III (EDI, EDII, and EDIII). EDI is a structurally central domain of the envelope protein which stabilizes the overall orientation of the protein, and the glycosylation sites in EDI are related to virus production, pH sensitivity, and neuroinvasiveness. EDII plays an important role in membrane fusion because of the immunodominance of the fusion loop epitope and the envelope dimer epitope. Additionally, EDIII is the major target of neutralization antibodies. The envelope protein is an important target for research to develop vaccine candidates and antiviral therapeutics. This review summarizes the structures and functions of ED I/II/III, and provides practical applications for the three domains, with the ultimate goal of implementing strategies to utilize the envelope protein against flavivirus infections, thus achieving better diagnostics and developing potential flavivirus therapeutics and vaccines.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17–36

Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17–36 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The currently available nonavalent human papillomavirus (HPV) vaccine exploits the highly antigenic L1 major capsid protein to promote high-titer neutralizing antibodies, but is limited to the HPV types included in the vaccine since the responses are highly type-specific. The limited cross-protection offered by the L1 virus-like particle (VLP) vaccine warrants further investigation into cross-protective L2 epitopes. The L2 proteins are yet to be fully characterized as to their precise placement in the virion. Adding to the difficulties in localizing L2, studies have suggested that L2 epitopes are not well exposed on the surface of the mature capsid prior to cellular engagement. Using a series of competition assays between previously mapped anti-L1 monoclonal antibodies (mAbs) (H16.V5, H16.U4 and H16.7E) and novel anti-L2 mAbs, we probed the capsid surface for the location of an L2 epitope (aa17–36). The previously characterized L1 epitopes together with our competition data is consistent with a proposed L2 epitope within the canyons of pentavalent capsomers.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years.
Ed Rybicki's insight:
Share your insight
more...
No comment yet.
Scooped by Denis Hudrisier
Scoop.it!

Multi-platform ’Omics Analysis of Human Ebola Virus Disease Pathogenesis

Multi-platform ’Omics Analysis of Human Ebola Virus Disease Pathogenesis | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Eisfeld et al. comprehensively evaluated changes in host molecules in plasma and peripheral
immune cells of Ebola virus disease (EVD) patients. Their results suggest new mechanisms
of EVD pathogenesis and putative biomarkers for predicting EVD outcomes. Moreover,
datasets associated with this work are an important community resource for further
research.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Phyx: phylogenetic tools for unix | Bioinformatics | Oxford Academic

Phyx: phylogenetic tools for unix | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract. Summary: The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic inve
more...
No comment yet.
Scooped by Denis Hudrisier
Scoop.it!

Does a sea of viruses inside our body help keep us healthy?

Does a sea of viruses inside our body help keep us healthy? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Study suggests people may absorb 30 billion bacteria-killing viruses every day
more...
No comment yet.
Rescooped by Kenzibit from Synthetic biology
Scoop.it!

Kill switches for engineered microbes gone rogue

Kill switches for engineered microbes gone rogue | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Synthetic biologists are fitting the genomes of microorganisms with synthetic gene circuits to break down polluting plastics, non-invasively diagnose and treat infections in the human gut, and generate chemicals and nutrition on long haul space flights. Although showing great promise in the laboratory, these technologies require control and safety measures that make sure the engineered microorganisms keep their functional gene circuits intact over many cell divisions, and that they are contained to the specific environments they are designed for.


Via Integrated DNA Technologies
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Poxviruses: Slipping and sliding through transcription and translation

Poxviruses: Slipping and sliding through transcription and translation | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Efficient comparative phylogenetics on large trees | Bioinformatics | Oxford Academic

Efficient comparative phylogenetics on large trees | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. - PubMed - NCBI

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Nat Commun. 2017 Nov 13;8(1):1455. doi: 10.1038/s41467-017-01542-z.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Cancer Immunotherapy Review
Scoop.it!

Migrating into the Tumor: a Roadmap for T Cells

Migrating into the Tumor: a Roadmap for T Cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Tumors can be divided into ‘hot’ (T cell inflamed) or ‘cold’ (T cell noninflamed)
according to the presence of immune cells. In this review, we discuss variables that
influence T cell migration into the tumor microenvironment. Chemokines can attract
T cells to the tumor site and tumor intrinsic pathways can influence the composition
of local chemokines. Tumor-induced vasculature can hamper T cell migration. Other
immune cells and tumor-derived molecules can block T cell proliferation and survival.

Via Krishan Maggon
more...
No comment yet.