<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/23680?offset=1350 https://bioinformaticsonline.com/bookmarks/view/37618/snakemake%E2%80%94a-scalable-bioinformatics-workflow-engine Sun, 02 Sep 2018 16:32:42 -0500 https://bioinformaticsonline.com/bookmarks/view/37618/snakemake%E2%80%94a-scalable-bioinformatics-workflow-engine <![CDATA[Snakemake—a scalable bioinformatics workflow engine]]> Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. 

Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

]]> Jit https://bioinformaticsonline.com/blog/view/39469/introduction-to-bioinformatics Wed, 05 Jun 2019 14:58:11 -0500 https://bioinformaticsonline.com/blog/view/39469/introduction-to-bioinformatics <![CDATA[Introduction to Bioinformatics]]> Introduction to Bioinformatics Course

Introduction to bioinformatics is a course for biologists and clinicians that would like to learn more about the way bioinformatics is used in healthcare, biotech and pharmaceuitcal industry as well as basic research. The course covers many of the topics transformed by the emergence of big data and computational technologies. To learn more about the course, visit: https://edu.t-bio.info/course/introduction-bioinformatics/

]]> eliabrodsky https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab Tue, 04 Feb 2020 06:27:02 -0600 <![CDATA[Liu Lab]]> Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

]]> https://bioinformaticsonline.com/bookmarks/view/41202/biocontainers Thu, 20 Feb 2020 05:29:46 -0600 https://bioinformaticsonline.com/bookmarks/view/41202/biocontainers <![CDATA[BioContainers]]> BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics packages (e.g conda) and containers (e.g docker, singularity). BioContainers is based on the popular frameworks Conda, Docker and Singularity.

Address of the bookmark: https://biocontainers.pro/#/

]]> Jit https://bioinformaticsonline.com/opportunity/view/42236/bioinformatics-focused-postdoctoral-fellow Fri, 23 Oct 2020 05:52:52 -0500 <![CDATA[Bioinformatics-focused postdoctoral fellow]]> Jason Thomas Ladner currently recruiting for a bioinformatics-focused postdoctoral
fellow to join the group at the Pathogen and Microbiome Institute,
Northern Arizona University (http://www7.nau.edu/ladnerlab/). This
will be a multi-year, NIH-funded position focused on the development and
utilization of a novel platform for highly multiplexed antiviral serology,
which utilizes high-throughput sequencing technology.

To apply:
https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=1&JobOpeningId=604999&PostingSeq=1

For more information, feel free to contact me: jason.ladner@nau.edu

]]> https://bioinformaticsonline.com/bookmarks/view/42552/bioinformatics-workbook Tue, 05 Jan 2021 22:42:32 -0600 https://bioinformaticsonline.com/bookmarks/view/42552/bioinformatics-workbook <![CDATA[bioinformatics workbook]]> This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is referred to for more information throughout the book.

https://bioinformaticsworkbook.org/

Address of the bookmark: https://bioinformaticsworkbook.org/

]]> biogeek https://bioinformaticsonline.com/opportunity/view/43284/tech-and-bioinformatics-roles-at-basepaws Wed, 18 Aug 2021 23:34:25 -0500 <![CDATA[Tech and Bioinformatics roles at Basepaws]]> Basepaws is an LA-based pet genomics company, quickly growing and focused on feline and canine at-home genetic and biome tests, along with many other projects and products in the works. Thank you for taking a look!

Bioinformatics : https://www.linkedin.com/jobs/view/2681785372/

Engineer: https://www.linkedin.com/jobs/view/2681796993/

]]> https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly Mon, 24 Jul 2023 07:04:26 -0500 https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly <![CDATA[Bioinformatics tools for genome assembly !]]> There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

  1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

  2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

  3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

  4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

  5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

  6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

  7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

  8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

  9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

  10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

  11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

  12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

  13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

  14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

  15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

  16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

]]> BioStar https://bioinformaticsonline.com/opportunity/view/44407/mopga-2024-visiting-fellowship-program-for-early-career-researchers Fri, 10 Nov 2023 02:30:22 -0600 <![CDATA[MOPGA 2024 Visiting Fellowship Program for Early Career Researchers]]> France, as a major player in the fight against climate change and guarantor of the spirit of the Paris Agreement, is launching a new MOPGA visiting fellowship program geared towards strengthening scientific contributions to climate change issues raised by the COPs.

This seventh Make Our Planet Great Again (MOPGA) call for applications is intended to welcome at least 40 early career researchers wishing to carry out their research in France. The program is funded by the French Ministry for Europe and Foreign Affairs, in collaboration with the French Ministry for Higher Education and Research, and implemented by Campus France.

The MOPGA 2024 Visiting Fellowship Program for Early Career Researchers will support researchers working on topics listed in the "Research Themes" section.

More at https://www.campusfrance.org/en/mopga-2024

]]> https://bioinformaticsonline.com/videolist/watch/10749/memories-can-be-passed-down-through-dna Sat, 10 May 2014 21:24:10 -0500 https://bioinformaticsonline.com/videolist/watch/10749/memories-can-be-passed-down-through-dna <![CDATA[Memories Can Be Passed Down Through DNA]]> The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com]]>