共查询到20条相似文献,搜索用时 281 毫秒
1.
Nomi L. Harris Peter J. A. Cock Hilmar Lapp Brad Chapman Rob Davey Christopher Fields Karsten Hokamp Monica Munoz-Torres 《PLoS computational biology》2016,12(2)
The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.Open in a separate window 相似文献
2.
Rupal Chauhan Yogesh Jasrai Himanshu Pandya Suman Chaudhari Chand Mal Samota 《Bioinformation》2014,10(9):595-598
Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique
bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism,
images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible
sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic
databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the
FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the
common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and
JAVA. FCDD is freely available.
Availability
http://www.fruitcropsdd.com/ 相似文献3.
A Genomic Target Database (GTD) has been developed having putative genomic drug targets for human bacterial pathogens. The selected
pathogens are either drug resistant or vaccines are yet to be developed against them. The drug targets have been identified using subtractive
genomics approaches and these are subsequently classified into
- Drug targets in pathogen specific unique metabolic pathways,
- Drug targets in host-pathogen common metabolic pathways, and
- Membrane localized drug targets.
Availability
GTD is available at IIOAB website http://www.iioab.webs.com/GTD.htm. It can also be accessed at http://www.iioabdgd.webs.com.GTD is free for academic research and non-commercial use only. Commercial use is strictly prohibited without prior permission from IIOAB. 相似文献4.
Chinnaiah Swaminathan Vinobha Maruthamuthu Rajadurai Ekambaram Rajasekaran 《Bioinformation》2008,3(2):98-99
The use of bioinformatics tools require different sequence formats at various instances. Every tool uses specific set of
formats for processing. Sequence in one format is often required in another format. Thus, there is a need for sequence
format conversion. A number of such tools are available in the public domain. Here, we describe BIOFFORC as a file format
converter. The tool is developed with a graphical user interface in PERL.
Availability
http://www.winningpath.com/biofforc/ 相似文献5.
Maria Pratheepa Sushil Kumar Jalali Robinson Silvester Arokiaraj Thiruvengadam Venkatesan Mandadi Nagesh Madhusmita Panda Sharath Pattar 《Bioinformation》2014,10(2):98-100
Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the
National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and
publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It
bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects.
IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client–
server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn
allows the registered users to input new information, search and view information related to DNA barcode of agriculturally
important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.
Availability
http://www.nabg-nbaii.res.in/barcode 相似文献6.
ChangKug Kim SooJin Kwon GangSeob Lee HwanKi Lee JiWeon Choi YongHwan Kim JangHo Hahn 《Bioinformation》2009,3(8):344-345
The AllergenPro database has developed a web-based system that will provide information about allergen in microbes, animals and plants. The database has three major parts and
functions:(i) database list; (ii) allergen search; and (iii) allergenicity prediction. The database contains 2,434 allergens related information readily available in the database
such as on allergens in rice microbes (712 records), animals (617 records) and plants (1,105 records). Furthermore, this database provides bioinformatics tools for allergenicity
prediction. Users can search for specific allergens by various methods and can run tools for allergenicity prediction using three different methods.
Availability
The database is available for free at http://www.niab.go.kr/nabic/ 相似文献7.
Dimitri Brosens Fran?ois Vankerkhoven David Ignace Philippe Wegnez Nicolas Noé André Heughebaert Jeannine Bortels Wouter Dekoninck 《ZooKeys》2013,(306):59-70
FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the ‘Gaspar’ Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year.The latest version of the dataset is publicly and freely accessible through this url: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.bePurpose: FORMIDABEL is a joint cooperation of the Flemish ants working group “Polyergus” (http://formicidae.be) and the Wallonian ants working group “FourmisWalBru” (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types.Open in a separate windowFigure 1.www.formicidae-atlas.be 相似文献
8.
Martina Kutmon Martijn P. van Iersel Anwesha Bohler Thomas Kelder Nuno Nunes Alexander R. Pico Chris T. Evelo 《PLoS computational biology》2015,11(2)
PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways.Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application.PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.
This is a PLOS Computational Biology software article.相似文献
9.
Luis N. Brand?o Rebecca Ferguson Irma Santoro Sue Jinks-Robertson Robert A. Sclafani 《Genetics》2014,197(4):1111-1122
The yeast Dbf4-dependent kinase (DDK) (composed of Dbf4 and Cdc7 subunits) is an essential, conserved Ser/Thr protein kinase that regulates multiple processes in the cell, including DNA replication, recombination and induced mutagenesis. Only DDK substrates important for replication and recombination have been identified. Consequently, the mechanism by which DDK regulates mutagenesis is unknown. The yeast mcm5-bob1 mutation that bypasses DDK’s essential role in DNA replication was used here to examine whether loss of DDK affects spontaneous as well as induced mutagenesis. Using the sensitive lys2ΔA746 frameshift reversion assay, we show DDK is required to generate “complex” spontaneous mutations, which are a hallmark of the Polζ translesion synthesis DNA polymerase. DDK co-immunoprecipitated with the Rev7 regulatory, but not with the Rev3 polymerase subunit of Polζ. Conversely, Rev7 bound mainly to the Cdc7 kinase subunit and not to Dbf4. The Rev7 subunit of Polζ may be regulated by DDK phosphorylation as immunoprecipitates of yeast Cdc7 and also recombinant Xenopus DDK phosphorylated GST-Rev7 in vitro. In addition to promoting Polζ-dependent mutagenesis, DDK was also important for generating Polζ-independent large deletions that revert the lys2ΔA746 allele. The decrease in large deletions observed in the absence of DDK likely results from an increase in the rate of replication fork restart after an encounter with spontaneous DNA damage. Finally, nonepistatic, additive/synergistic UV sensitivity was observed in cdc7Δ pol32Δ and cdc7Δ pol30-K127R,K164R double mutants, suggesting that DDK may regulate Rev7 protein during postreplication “gap filling” rather than during “polymerase switching” by ubiquitinated and sumoylated modified Pol30 (PCNA) and Pol32. 相似文献
10.
Bipin P. Kulkarni Sona B. Nair Manasi Vijapurkar Leenam Mota Sharda Shanbhag Shehnaz Ali Shrimati D. Shetty Kanjaksha Ghosh 《PloS one》2014,9(10)
Background
Though rare in occurrence, patients with rare bleeding disorders (RBDs) are highly heterogeneous and may manifest with severe bleeding diathesis. Due to the high rate of consanguinity in many caste groups, these autosomal recessive bleeding disorders which are of rare occurrence in populations across the world, may not be as rare in India.Objectives
To comprehensively analyze the frequency and nature of mutations in Indian patients with RBDs.Methods
Pubmed search was used (www.pubmed.com) to explore the published literature from India on RBDs using the key words “rare bleeding disorders”, “mutations”, “India”, “fibrinogen”, “afibrinogenemia”, “factor II deficiency”, “prothrombin” “factor VII deficiency”, “factor V deficiency”, “factor X deficiency”, “factor XI deficiency”, “combined factor V and VIII deficiency”, “factor XIII deficiency”, “Bernard Soulier syndrome” and “Glanzmanns thrombasthenia” in different combinations. A total of 60 relevant articles could be retrieved. The distribution of mutations from India was compared with that of the world literature by referring to the Human Gene Mutation Database (HGMD) (www.hgmd.org).Results
Taken together, 181 mutations in 270 patients with different RBDs have been reported from India. Though the types of mutations reported from India and their percentage distribution with respect to the world data are largely similar, yet much higher percentage of small deletions, duplication mutations, insertions, indels were observed in this analysis. Besides the identification of novel mutations and polymorphisms, several common mutations have also been reported, which will allow to develop a strategy for mutation screening in Indian patients with RBDs.Conclusion
There is a need for a consortium of Institutions working on the molecular pathology of RBDs in India. This will facilitate a quicker and cheaper diagnosis of RBDs besides its utility in first trimester prenatal diagnosis of the affected families. 相似文献11.
12.
Shanmugam Anandakumar Saravanan Vijayakumar Nagarajan Arumugam M Michael Gromiha 《Bioinformation》2015,11(11):512-513
Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals.
This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function
about mammalian ncRNAs.
Availability
The database is available for free at http://www.iitm.ac.in/bioinfo/mmndb/ 相似文献13.
Veljko Veljkovic Nevena Veljkovic Slobodan Paessler Marco Goeijenbier Vladimir Perovic Sanja Glisic Claude P. Muller 《PloS one》2016,11(11)
Influenza A virus (IAV) subtypes against which little or no pre-existing immunity exists in humans represent a serious threat to global public health. Monitoring of IAV in animal hosts is essential for early and rapid detection of potential pandemic IAV strains to prevent their spread. Recently, the increased pandemic potential of the avian-like swine H1N1 IAV A/swine/Guangdong/104/2013 has been suggested. The virus is infectious in humans and the general population seems to lack neutralizing antibodies against this virus. Here we present an in silico analysis that shows a strong human propensity of this swine virus further confirming its pandemic potential. We suggest mutations which would further enhance its human propensity. We also propose conserved antigenic determinants which could serve as a component of a prepandemic vaccine. The bioinformatics tool, which can be used to further monitor the evolution of swine influenza viruses towards a pandemic virus, are described here and are made publically available (http://www.vin.bg.ac.rs/180/tools/iav_mon.php; http://www.biomedprotection.com/iav_mon.php). 相似文献
14.
Small nucleolar ribonucleoproteins (snoRNPs) are widely studied and characterized as guide RNAs for sequence-specific 2′-O-ribose methylation and psuedouridylation of ribosomal RNAs. In addition, snoRNAs have also been shown to interact with some tRNAs and direct alternative splicing in mRNA biogenesis. Recent advances in bioinformatics have resulted in new algorithms able to rapidly identify noncoding RNAs generally and snoRNAs specifically in genomic and metagenomic sequences, resulting in a rapid increase in the number and diversity of identified snoRNA sequences. The snoRNP database is a web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. The database currently contains 8994 snoRNA sequences from Bacteria, Archaea, and Eukaryotes and 589 snoRNA-associated protein sequences. The snoRNP database can be found at: http://evolveathome.com/snoRNA/snoRNA.php. 相似文献
15.
Andrew K Benson 《Genome biology》2015,16(1)
Comparative analyses of the control of mammalian microbiomes by host genetic architecture reveal striking conserved features that have implications for the evolution of host–microbiome interactions.See related Research article: http://www.genomebiology.com/2015/16/1/191 相似文献
16.
Padmaja L. Ghospurkar Timothy M. Wilson Amber L. Severson Sarah J. Klein Sakina K. Khaku André P. Walther Stuart J. Haring 《Genetics》2015,199(3):711-727
In response to DNA damage, two general but fundamental processes occur in the cell: (1) a DNA lesion is recognized and repaired, and (2) concomitantly, the cell halts the cell cycle to provide a window of opportunity for repair to occur. An essential factor for a proper DNA-damage response is the heterotrimeric protein complex Replication Protein A (RPA). Of particular interest is hyperphosphorylation of the 32-kDa subunit, called RPA2, on its serine/threonine-rich amino (N) terminus following DNA damage in human cells. The unstructured N-terminus is often referred to as the phosphorylation domain and is conserved among eukaryotic RPA2 subunits, including Rfa2 in Saccharomyces cerevisiae. An aspartic acid/alanine-scanning and genetic interaction approach was utilized to delineate the importance of this domain in budding yeast. It was determined that the Rfa2 N-terminus is important for a proper DNA-damage response in yeast, although its phosphorylation is not required. Subregions of the Rfa2 N-terminus important for the DNA-damage response were also identified. Finally, an Rfa2 N-terminal hyperphosphorylation-mimetic mutant behaves similarly to another Rfa1 mutant (rfa1-t11) with respect to genetic interactions, DNA-damage sensitivity, and checkpoint adaptation. Our data indicate that post-translational modification of the Rfa2 N-terminus is not required for cells to deal with “repairable” DNA damage; however, post-translational modification of this domain might influence whether cells proceed into M-phase in the continued presence of unrepaired DNA lesions as a “last-resort” mechanism for cell survival. 相似文献
17.
In computational science literature including, e.g., bioinformatics, computational statistics or machine learning, most published articles are devoted to the development of “new methods”, while comparison studies are generally appreciated by readers but surprisingly given poor consideration by many journals. This paper stresses the importance of neutral comparison studies for the objective evaluation of existing methods and the establishment of standards by drawing parallels with clinical research. The goal of the paper is twofold. Firstly, we present a survey of recent computational papers on supervised classification published in seven high-ranking computational science journals. The aim is to provide an up-to-date picture of current scientific practice with respect to the comparison of methods in both articles presenting new methods and articles focusing on the comparison study itself. Secondly, based on the results of our survey we critically discuss the necessity, impact and limitations of neutral comparison studies in computational sciences. We define three reasonable criteria a comparison study has to fulfill in order to be considered as neutral, and explicate general considerations on the individual components of a “tidy neutral comparison study”. R codes for completely replicating our statistical analyses and figures are available from the companion website http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/plea2013. 相似文献
18.
GuiPeng Li Ming Li YiWei Zhang Dong Wang Rong Li Roger Guimerà Juntao Tony Gao Michael Q. Zhang 《PloS one》2014,9(5)
Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by “User Guide” in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user’s own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID.
Availability
ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request. 相似文献19.
A database providing information on mosquito specimens (Arthropoda: Diptera: Culicidae) collected in French Guiana is presented. Field collections were initiated in 2013 under the auspices of the CEnter for the study of Biodiversity in Amazonia (CEBA: http://www.labexceba.fr/en/). This study is part of an ongoing process aiming to understand the distribution of mosquitoes, including vector species, across French Guiana. Occurrences are recorded after each collecting trip in a database managed by the laboratory Evolution et Diversité Biologique
(EDB), Toulouse, France. The dataset is updated monthly and is available online. Voucher specimens and their associated DNA are stored at the laboratory Ecologie des Forêts de Guyane
(Ecofog), Kourou, French Guiana. The latest version of the dataset is accessible through EDB’s Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=mosquitoes_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/5a8aa2ad-261c-4f61-a98e-26dd752fe1c5 It can also be viewed through the Guyanensis platform at http://guyanensis.ups-tlse.fr 相似文献
20.
Padavala Ajay Babu Suma Sree Puppala Satyavarapu Lakshmi Aswini Metta Ramya Vani Chinta Narasimha Kumar Tallapragada Prasanna 《Bioinformation》2008,3(3):142-143
Marine compound database consists of marine natural products and chemical entities, collected from various literature sources,
which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories
of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial
information. The database is freely available online and can be accessed at
http://www.progenebio.in/mcdb/index.htm 相似文献