<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27331?offset=550 https://bioinformaticsonline.com/blog/view/33629/list-of-universities-offering-bachelor-master-or-phd-bioinformatics-degree-in-malaysia Thu, 22 Jun 2017 01:34:02 -0500 https://bioinformaticsonline.com/blog/view/33629/list-of-universities-offering-bachelor-master-or-phd-bioinformatics-degree-in-malaysia <![CDATA[List of universities offering Bachelor, Master or PhD bioinformatics degree in Malaysia]]> Bioinformatics is a newly emerging interdisciplinary research area, which may be defined as the ―interface between biological and computational sciences. Most of the Bioinformatics work that is done can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. The global Bioinformatics industry has grown at a double-digit growth rate in the past and is expected to follow the same pattern in the next four years. US remains the largest market in the world, but Asia-Pacific countries, particularly India and China, are witnessing the fastest growth and are anticipated to emerge as the dominating forces in future. The Comparison of Bioinformatics Industry between Malaysia, India and other countries are discussed in this http://ijbssnet.com/journals/Vol.%202_No._10;_June_2011/11.pdf paper.

Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper. Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:

3 program(s) at AIMST University, Malaysia

Master of Science in Biotechnology (MSc) - Bioinformatics by Research

Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research

Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research

 

1 program(s) at INTI International University and Colleges, Malaysia

American Degree Transfer Program (Biosciences) in Bioinformatics

 

3 program(s) at Management and Science University (MSU), Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

 

1 program(s) at Multimedia University (MMU), Malaysia

Bachelor of Science (Honours) Bioinformatics

 

1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus, Malaysia

Bachelor of Bioinformatics (Hons)

 

2 program(s) at Universiti Malaysia Sabah (UMS), Malaysia

PhD - Doctor of Philosophy in Bioinformatics (By Research)

MSc - Master of Science in Bioinformatics (By Research)

 

6 program(s) at Universiti Putra Malaysia (UPM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master of Science in Bioinformatics and System Biology by Research

Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics by Research

PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research

 

1 program(s) at Universiti Selangor (UNISEL), Malaysia

Bachelor of Bioinformatics (Hons)

 

3 program(s) at Universiti Teknologi Malaysia (UTM), Malaysia

M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research

PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research

Bachelor of Computer Science (BioInformatics)

 

4 program(s) at University of Malaya (UM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master in Bioinformatics by Coursework

PhD - Doctor of Philosophy in Bioinformatics by Research

Bachelor of Science (BSc) in Bioinformatics

 

3 program(s) at Perdana University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

 

3 program(s) at Monash University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

 

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.

]]> sahabuddin https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome Thu, 08 Aug 2024 23:31:18 -0500 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome <![CDATA[Tools to access the quality of your assembled genome !]]>
  • FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
  • GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
  • ASSEMBLATHON STATS: Assembly statistics
  • GENOMETOOLS GT STAT: Annotation statistics
  • NCBI FCS ADAPTOR: Adaptor contamination pass/fail
  • NCBI FCS GX: Foreign organism contamination pass/fail
  • BUSCO: Gene-space completeness estimation
  • TIDK: Telomere repeat identification
  • LAI: Continuity of repetitive sequences
  • KRAKEN2: Taxonomy classification
  • HIC CONTACT MAP: Alignment and visualisation of HiC data
  • MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
  • MERQURY: K-mer completeness, consensus quality and phasing assessment
    • ]]>     LEGE     https://bioinformaticsonline.com/opportunity/view/21685/uiar-short-term-trainingfinal-year-dissertation-project-in-life-sciencesbioinformaticsbiotech Mon, 16 Mar 2015 23:56:25 -0500 <![CDATA[UIAR Short-Term Training/Final Year Dissertation Project in Life Sciences/Bioinformatics/Biotech]]> Short-term training/Final year dissertation project

    Candidates desirous of doing a short-term training / final year dissertation project for MSc (Life Sciences/Bioinformatics/Biotechnology or any science discipline) at UIAR Biophysics and Bioinformatics department may please drop an email atanju@iiar.res.in along with their resume.

    Selected candidates will be further intimated. There will be a fees charged for doing the project at UIAR. The projects will be experimental or computational or involve both.

    The training scope will be in the following areas but not limited to:

    Bioinformatics analysis, Docking and Virtual screening, Molecular Dynamics simulation, Cloning, expression and purification of proteins, Biophysical and Biochemical characterisation of proteins, Crystallization and Structural Studies.

    Advertisement: www.iiar.res.in/?q=node/450

    ]]>         https://bioinformaticsonline.com/blog/view/45270/when-dna-data-tells-the-wrong-story-crossfit-assist-to-resolve Fri, 04 Sep 2026 03:41:38 -0500 https://bioinformaticsonline.com/blog/view/45270/when-dna-data-tells-the-wrong-story-crossfit-assist-to-resolve <![CDATA[When DNA Data Tells the Wrong Story - CrossFit assist to resolve !]]> Imagine comparing humans and chimpanzees to discover which genes make us different. You have millions of RNA-sequencing reads—but there is a catch: the computer may align these reads more easily to one species' genome than the other.

    Suddenly, a technical error can look like a biological difference.

    This is the problem Kenneth A. Barr and Yoav Gilad tackle with CrossFilt, a new computational tool introduced in Genome Biology journal.

    CrossFilt acts like a careful referee. It keeps only sequencing reads that can be reliably compared across species, filtering out reads that could create alignment bias.

    When tested on human, chimpanzee, and rhesus macaque data, CrossFilt reduced false discoveries and produced more reliable cross-species comparisons.

    The message is simple: before asking what makes species different, we need to make sure our methods aren't creating those differences.

    In genomics, sometimes the most important discovery is finding—and removing—the bias hiding in the data.

    Read more at https://link.springer.com/article/10.1186/s13059-026-04082-2?

    ]]>     BioStar     https://bioinformaticsonline.com/opportunity/view/21894/bioinformatics-engineer-algorithm-development Wed, 01 Apr 2015 21:39:05 -0500 <![CDATA[Bioinformatics Engineer -- Algorithm Development]]> Centrillion Biosciences is a venture backed life sciences company located in Palo Alto, California. The company provides high quality genomic services to academic and industrial customers including top universities and research institutes. Centrillion Biosciences has an immediate opening for a full-time Bioinformatics Engineer. We're looking for an energetic, innovative, and motivated person who works well independently and on teams. The ideal candidate will have experience designing and implementing efficient algorithms to process large datasets. The role will involve collaborating with research scientists and other engineers, so strong communication skills are a must.

    Job Description

    • Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
    • Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
    • Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
    • Build simulation algorithms to help guide and analyze research done in the lab
    • Solve challenging engineering problems that require the development of innovative algorithms

    Requirements

    • Strong background in mathematics/statistics with a degree in a related field
    • Strong analytical, coding, communication, and organizational skills
    • Experience with algorithm development, simulations, and data analysis
    • Proficiency in at least one modern programming language (like Python or Perl)
    • Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
    • Experience with machine learning and pattern recognition is preferred

    Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.

    ]]>         https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

    Sample Circleator image

    Common uses of the tool include:

    • Displaying the sequence and/or genes in a GenBank flat file.
    • Highlighting differences and/or similarities in gene content between related organisms.
    • Comparing SNPs and indels between closely-related strains or serovars.
    • Comparing gene expression values across multiple samples or timepoints.
    • Visualizing coverage plots of RNA-Seq read alignments.

    Key Features

    Circleator...

    • Builds on BioPerl and the input file formats that it supports, including:
    • Accepts a number of other commonly-used datatypes and file formats:
      • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
    • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
    • Requires only a single configuration file whose layout mirrors that of the figure itself.
      • Predefined configuration files and "track" types are supplied for common datasets.
      • Advanced features allow limited analyses to be performed as a figure is drawn.
    • Includes an extensive set of regression tests.
    • Offers a prototype web-based GUI (under the "Ringmaster" project.)

    https://github.com/jonathancrabtree/Circleator

    Address of the bookmark: https://github.com/jonathancrabtree/Circleator

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/22283/iihr-recruitment-2015-%E2%80%93-srf-project-asst-research-associate-posts Wed, 06 May 2015 06:13:26 -0500 <![CDATA[IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts]]> IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts: ICAR-Indian Institute of Horticultural Research (IIHR) has published a notification for the recruitment of Senior Research Fellow, Project Assistant and Research Associate vacancies on temporary basis. Eligible candidates may apply in prescribed application format on or before 15-05-2015. Other details like age, educational qualification, selection process, how to apply are given below…

    IIHR Vacancy Details:
    Total No. of Posts: 14
    Name of the Post:
    1. Senior Research Fellow: 12 Posts
    2. Project Assistant: 01 Post
    3. Research Associate: 01 Post

    Age Limit: Candidates age limit is 40 years for men & 45 years for women for RA post, 35 years for men & 40 years for women for SRF post, 30 years for men & 35 years for women for JRF post and 21 to 40 years for Other as on closing date of receipt of applications. Age relaxation is applicable as per rules.

    Educational Qualification: Candidates should possess M.Sc (Ag) Plant Pathology or Microbiology or Biotechnology or Biochemistry or M.Tech (Ag) or Bioinformatics for SRF Posts, 10th class with experience in workshop (welding fitting) for Project Asst Post and M.Sc (Ag) Plant Pathology or M.Sc (Ag) Biotechnology or Ph.D in Plant Pathology or Agricultural Biotechnology for RA Post.

    Selection Process: Candidates will be selected based on their performance in interview.

    How to Apply: Eligible candidates may send their application in the prescribed format along with attested copies of relevant certificates and should mention name of PI/ Co-PI, Item No. of the Post & name of the post clearly on the application as well as on the cover to the Concerned PI/ Co-PI, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru-560089 on or before 15-05-2015 and attend the interview along with originals, two passport size photographs on 26 & 27-05-2015 from 10:00 AM Onwards.

    Important Dates:
    Last Date for Receipt of Applications: 15-05-2015.
    Date & Time of Interview: 26 & 27-05-2015 from 10:00 AM Onwards.
    Venue: IIHR Campus.

    More at http://www.iihr.ernet.in/content/srf-jrf-application-format

    ]]>         https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly Wed, 06 Dec 2017 02:08:14 -0600 https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly <![CDATA[COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly]]> An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

    Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

    ]]>     Jit     https://bioinformaticsonline.com/news/view/22017/binc-2015 Sat, 11 Apr 2015 20:35:27 -0500 https://bioinformaticsonline.com/news/view/22017/binc-2015 <![CDATA[BINC 2015 !!!]]> Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration will open from March 9,2015 to April 30,2015. Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcutta University, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati. In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

    More at http://www.binc.co.in/College/Index_New.aspx

    BINC notification http://www.binc.co.in/PdfDocuments/Notification.pdf

    Few dates to remember:

    Starting of online submission of application: March 9, 2015
    Last date for submission of application: April 30,2015
    Examination consists of two parts:
    Part I (Paper I) : June 7, 2015 (10 AM-12 PM)
    Part II ( Paper II & III) :June 28, 2015 (9 AM-12 PM & 2 PM-4 PM)

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool Sun, 10 Dec 2017 17:03:48 -0600 https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool <![CDATA[Synima: Synteny Imaging tool]]> 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.

    Address of the bookmark: https://github.com/rhysf/Synima

    ]]>     Jit