BOL: Related items

Clinical Genomics & Informatics Europe at Lisbon, Portugal

Wed, 14 Aug 2013 09:58:34 -0500

Bio-IT World and Cambridge Healthtech Institute's fifth international Clinical Genomics & Informatics Europe conference will feature four main tracks on Clinical Exome Sequencing, High Scale Computing, Genome Informatics, and RNA-Seq and Transcriptome Analysis, as well as two pre-conference symposia on Clinical Epigenetics and Quantitative Digital Detection Technologies. The conference will tackle the huge amounts of sequencing data produced by new technologies that have introduced significant challenges for bioinformatics, both in terms of the analysis and interpretation of data and clinical implementation of novel variants. Members of the international community will come together to look at the science and informatics required to utilize next generation sequencing for the molecular diagnosis of complex diseases.

Dated : 04 Dec 2013 - 06 Dec 2013

More at : http://www.clinicalgenomicsinformatics.com/

7th International Conference on Bioinformatics and Computational Biology (BICoB)

Rahul Agarwal — Mon, 06 Oct 2014 16:19:36 -0500

In recent years, computational biology and medical informatics have seen significant advances driven by computational techniques in bioinformatics making bioinformatics and computational biology among the most vibrant research areas. The 7th international conference on Bioinformatics and Computational Biology (BICoB-2015) provides an excellent venue for researchers and practitioners in the fields of bioinformatics and computational biology to present and publish their research results and techniques. The BICoB conference seeks original and high quality papers in the fields of bioinformatics, computational biology, systems biology, medical informatics and the related disciplines. We also encourage work in progress and research results in the emerging and evolutionary computational areas. Computational techniques have already enabled unprecedented advances in modern biology and medicine. Work in the computational methods related to, or with application in, bioinformatics is also encouraged including: data mining, text mining, machine learning, modeling and simulation, pattern recognition, data visualization, biostatistics, .etc. The topics of interest include (and are not limited to):
Genome analysis: Genome assembly, genome annotation, gene finding, alternative splicing, EST analysis and comparative genomics.
Sequence analysis: Multiple sequence alignment, sequence search and clustering, function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences.
Phylogenetics: Phylogeny estimation, models of evolution, comparative biological methods, population genetics.
Structural Bioinformatics: Structure matching, prediction, analysis and comparison; methods and tools for docking; protein design
Analysis of high-throughput biological data: Microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS, proteomics, mass spectrometry.
Genetics and population analysis: Linkage analysis, association analysis, population simulation, haplotyping, marker discovery, genotype calling.
Systems biology: Systems approaches to molecular biology, multiscale modeling, pathways,gene networks.
Computational Proteomics: Filtering and indexing sequence databases, Peptide quantification and identification, Genome annotations via mass spectrometry, Identification of post-translational modifications, Structural genomics via mass spectrometry, Protein-protein interactions, Computational approaches to analysis of large scale Mass spectrometry data, Exploration and visualization of proteomic data, Data models and integration for proteomics and genomics, Querying and retrieval of proteomics and genomics data etc.

Authors of selected high quality papers in BICoB-2015 will be invited to submit extended version of their papers for possible publication in bioinformatics journals (Journal of Bioinformatics and Computational Biology JBCB).

Deadlines:

Paper Submission Deadline October 24, 2014
Notification of Acceptance December 15, 2014
Camera-Ready Manuscript January 16, 2015

Address of the bookmark: http://www.cs.umb.edu/bicob/

Marie Curie PhD position available immediately

Fri, 24 Apr 2015 09:23:57 -0500

Sub-project 10: Development of bioinformatic tools for the analysis of MACE data
Host Organizations GenXPRO (Germany)
Objectives : The ESR will be in charge of standardising pipelines that will be used for RNA-seq and MACE analyses by all the participants. He will be involved in performing next generation sequencing to characterise environmental adaptation. A single pipeline to analyse listerial transcriptomic and proteomic data will be developed and implemented by each partner for the sake of uniformity of all the data produced within List_MAPS. The ESR will be involved in the interpretation of transcriptomic and proteomic data for which pathway analyses and good data visualization will be required. A cytoscape app will be developed as visualization tool.
Expected Results: MACE analysis pipeline. Database. Transcriptome comparisons in selected habitats. Data visualization tool.
Duration (months) 24
Contact Dr. Bjorn ROTTER: rotter@genxpro.de

11. Development of innovative tools for rapid phenotypic characterisation of intraspecific diversity of Listeria monocytogenes (Joint supervision PhD)
Host Organizations BioFilm Control (France) and GenXPRO (Germany)
Objectives
1. The ESR will develop an assay to test biofilm phenotype in a large array of food processing-related environmental conditions (salt, acides, disinfectants, preservatives) in BFC facilities. He will be in charge of the development and validation of an in silico virulence assay. This assay will target specific mRNAs in order to estimate the virulence potential of strains of L. monocytogenes. Transcript targets will be selected and tested by qPCR in GXP premises. In the process of validation, virulence results of several strains collected in a humanised mouse model will be compared with the in silico analysis. Once these innovative tools will be validated, intraspecific phenotypic diversity (biofilm and virulence) will be assessed on a collection of environmental and clinical isolates of L. monocytogenes. Genotypic diversity will be assessed under the supervision of GPX.
Expected Results : Adaptation of the BioFilm Ring test R to test food processing environmental conditions. Development of an innovative in silico virulence assay surrogate to animal models. Diversity results will inform stakeholders on the level of health hazard according to the strain. This in turn will help secure food safety all along the shelf life of foodstuff.
Duration (months) 36
Contact : Dr. Thierry BERNARDI: thbe@biofilmcontrol.com
Dr. Bjorn ROTTER: rotter@genxpro.de
ELIGIBLE CRITERIA of Marie Sklokowska Curie actions:
Researchers may be of any nationality
Candidates shall at the time of recruitment by the host organization, be in the first four years (full-time equivalent research experience) of their research careers. Full-time equivalent research experience is measured from the date when a researcher obtained the degree which would formally entitle him or her to embark on a doctorate, either in the co

Computer Theory & Genetics: George Chao at TEDxUMNSalon

Thu, 15 Aug 2013 22:08:10 -0500

George Chao is an undergraduate senior studying Genetics and Computer Science at the University of Minnesota. Having started genetics research as soon as he entered the university, he has worked in labs spanning multiple disciplines as well as in Japan. Some of these researches include developmental genetics in Drosophila, computational techniques for analyzing protein interactions, and helping with the development of algorithms to analyze motion capture data of patients with neck pain. During this time, George steadily developed a fascination with the field of bioinformatics, the study of using computational techniques to learn from genetic data. He would like to go into a career of research into the application of bioinformatics in various fields. ---- The individuals involved with TEDxUMN have a passion for bringing together the great thinkers at the University of Minnesota and giving them the opportunity to share their ideas worth spreading and to discuss our shared future. We provide these great people the opportunity to share these ideas on a global stage and with an incredibly diverse audience. We believe in the power of ideas to change attitudes, lives and ultimately the world. Check out TEDxUMN at http://www.TEDxUMN.com/ In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

Candidates required in Bioinformatics and Genomics UK ONLY

Fri, 03 Jul 2015 08:22:41 -0500

I have various permanent positions available based in London, Manchester, Herftfordshire, Oxford and Belfast, as well as other areas throughout the UK.

If you are looking for a new opportunity and have skills within any sector of Bioinformatics with an IT skill then I would love to hear from you. I have various exciting opportunities from programmers to researchers to scientists.

Call me now on 01772 278050 or email me your cv and requirements and I will call you back dareen.evans@itworkshealth.co.uk

Mobyle: a new full web bioinformatics framework

Jit — Sun, 07 Jan 2018 19:33:45 -0600

Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/25/22/3005/179064

Dynamic Programming Alignment

Thu, 22 Aug 2013 09:38:28 -0500

lecture 9, Chem. C100, Spring 2013, UCLA

scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

Jit — Fri, 02 Mar 2018 04:29:47 -0600

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

PhD position in biochemistry towards bioinformatics at the Department of Biochemistry and Biophysics.

Tue, 03 Sep 2013 06:09:03 -0500

PhD position in biochemistry towards bioinformatics at the Department of Biochemistry and Biophysics. Reference number: SU FV-2293-13. Deadline for application: September 10, 2013.

Project title: Functional Inference from Domain Architecture and Orthology

Requirements

To be accepted as a PhD student, credits corresponding to four years of full-time studies at the undergraduate level are required, including credits corresponding to at least two years of fulltime studies in chemistry, life sciences or physics, depending on the program. The credits should include courses at the advanced level (second cycle) corresponding to one year and of these one semester should be a degree thesis. In order to facilitate the evaluation of merits and suitability for the PhD studies the curriculum vitae (CV) should contain information about the extent and focus of the academic studies. The quantity (as part of an academic year) and the quality mark of courses in chemistry and physics are of particular interest. The title, number of credits and the length in full-time months of undergraduate thesis and project work, should be specified.

Information

More information about the project can be provided by the project leader. General information about the PhD training program may be requested from the director of graduate studies, Stefan Nordlund, stefan@dbb.su.se or from Lena Mäler, Head of Department (prefekt), lenam@dbb.su.se

Further information on the web:

The Department of Biochemistry and Biophysics: www.dbb.su.se

Stockholm University: www.su.se/english

Faculty of Science: www.science.su.se/english

The handbook for postgraduate students: www.doktorandhandboken.nu/english

Application The application should contain a personal letter (a letter of intent explaining why you are interested in the specific project, why you are interested in studying for a PhD, what you hope to accomplish during your PhD studies, and what skills you can bring to this project), a curriculum vitae, a list of two persons who may act as referees (with telephone numbers and e-mail addresses), copies of degree certificates and transcripts of academic records, and a copy of your undergraduate thesis and articles, if any.

In order to apply for this position, please use the Stockholm University web-based application form (where it is possible to select language):

To the application form for this position.

Welcome with your application no later than September 10, 2013.

Project leader: Erik Sonnhammer, Erik.Sonnhammer@sbc.su.se,
www.sonnhammer.sbc.su.se

Advertisement: http://www.su.se/english/about/vacancies/phd-studies/phd-position-in-biochemistry-towards-bioinformatics-1.143446

Popular bioinformatics educational resources !

Rahul Nayak — Fri, 04 May 2018 19:43:21 -0500

Followings are the list of popular bioinformatics educational resources

Bii.a-star.edu.sg

Bio research and development. Has course information and research information.

Isb-sib.ch

SIB operates the ExPASy proteomics server and the Swiss node of EMBnet. Teaching activities include a series of post-graduate courses given at the Universities of Geneva and Lausanne, as well as at the EPFL, and a Masters Degree in bioinformatics. Major research areas include the development of integrated databases and software resources in the field of proteomics.

Bioinformatics.ca

Provides information about bioinformatics in Canada. Workshops, certification and resources.

Chickscope.beckman.uiuc.edu

Students raise chicken embryos in the classroom and obtain magnetic resonance images through the Internet.

Bcb.iastate.edu

Graduate program at Iowa State University offering Undergraduate Major (BCBio) and the PhD program (BCB).

Bu.edu/bioinformatics/

Interdisciplinary PhD and Masters Programs that include an internship in the local industry companies. In conjunction with the NE masters program.

Bioinformatics.ubc.ca

A computational biology research centre covering many areas of genomics, proteomics, computer science and statistics. Research, training, news and events, resources and support, director's message, faculty and personnel.

Openhelix.com

Provides onsite training on specific bioinformatics databases and tools. Also offers bioinformatic software testing and research consulting services.

Igb.uci.edu

Specializing in making publicly available software and database services for computational biology.

Bioinformatics.pe.kr

Maintained by Dr. Seyeon Weon, Korea providing information on courses, a database archive, software archive and online resources.

Groups.yahoo.com/group/bimatics/

Bioinformatics group for students interested and/or working in the bioinformatics/computationalbiology fields. Offers opportunities to exchanging information and sharing ideas.

Ncbi.nlm.nih.gov/books/NBK22183/

Information about several medically important genes and related diseases. Illustrates the use of bioinformatics in their study.

Bioinfo.mbb.yale.edu/mbb452a/2003/

Bioinformatics course at Yale University. All course slides are available online.

Cs.iastate.edu/~honavar/comp-bio-courses.html

Listing of computational molecular biology course pages that have extensive online course materials.

Bioinf.manchester.ac.uk/dbbrowser/bioactivity/prefacefrm.html

A web-based tutorial associated with "Introduction to bioinformatics" published by Addison Wesley Longman.

Northeastern.edu/bioinformatics/

From the Biology department and in cooperation with Boston University. Emphasis on the ability to integrate knowledge from biological, computational, and mathematical disciplines.

Biocomp.unibo.it/lsbioinfo/

A two year, international master's programme in bioinformatics at the Universita di Bologna, Italy.

Cs.helsinki.fi/bioinformatiikka/mbi/programme.html

A two year Masters Degree Programme in Bioinformatics (MBI) offered by the University of Helsinki and Helsinki University of Technology, Finland.

Ornl.gov/sci/techresources/Human_Genome/education/education.shtml

A resource for introductory information on the Human Genome Project.

His.se/bioinformatics

A one-year, international master's programme in bioinformatics at the University of Skovde, Sweden.

Members.tripod.com/C.elegans/

Resources in biochemical, molecular, cellular, system, and organism biology, including over 25,000 indexed links, accumulated since 2000, from topic menus or from search interface.

Bioinformatics.org/faq/#contents

Summary of basics of bioinformatics for the intelligent newcomer.

Jiscmail.ac.uk/archives/bioinformatics.html

Forum featuring various aspects, events and developments in the bioinformatics field.

Biinoida.blogspot.com

Blog focusing on bioinformatics, biotechnology, pharma regulatory affairs, IPR and clinical trials.

Colorbasepair.com/bioinformatics_courses_tutorials.html

A list of on-line course materials and tutorials for bioinformatics and computational biology.

Geospiza.com/education/

Instructional materials for teaching bioinformatics. These include animated tutorials on topicssuch as BLAST, finding mutations in a protein, and graphing with MS-Excel.

Bioinformatics.fi

An international, two-year Master's programme jointly managed by the University of Tampere and the University of Turku, Finland.

Perlsource.net

Provides online courses in Perl programming for bioinformatic tools.