ABRF 2019: Immuno-biotechnology and bioinformatics in Community Colleges

ABRF 2019: Immuno-biotechnology and bioinformatics in Community Colleges: Join us at the ABRF annual meeting for a poster presentation on Immuno-biotech and bioinformatics. Abstract Immuno-biotechnology and bioinformatics in Community Colleges By: Todd M. Smith, Sandra G. Porter, Dina Kovarik Digital World Biology and Shoreline Community College | Read More

Bio Databases 2019: Immunology

Bio Databases 2019: Immunology: DWBio.com Science Blog | I always look forward to sharing the Nucleic Acids Research (NAR) database issue. This year's blog topic is immunology. The NAR archive lists 31 immunologic databases, but only seven or so are active, and others are not listed in the NAR archive. Read the blog learn more.

How is a bioinformatician like Odysseus?

How is a bioinformatician like Odysseus?: DWBio.com Science Blog | Bioinformatics is full of unexpected adventures. Some are related to data discoveries, but many more are related to navigating the maize of software needed to implement a solution. | Immuno-bioinformatics, Immunoprofiling, Shoreline Community College ... Read More

Turning into pumpkins with Molecule World

Turning into pumpkins with Molecule World: DWBio.com Science Blog | A fun thing we can do with molecular models is to create art. In Molecule World™, the residue coloring option applies a different color to each amino acid and nucleotide.  When we're characterizing a protein and trying to understand its function, the residue coloring option helps us identify repetitive or unusual amino acid sequences, but we can also ...

Singularity: can it go to infinity?

Singularity: can it go to infinity?: Singularity: the point at which a function takes an infinite value.

"Eew!" Is how high performance computing (HPC) admins react to Docker, according to Dr. Vanessa Saurus when she described the motivation for developing Singularity [1] at the Cyverse Container Camp(link is external).  Like Docker, Singularity allows one to package programs and their dependencies in ways that they can be run as virtual instances with low overhead. Singularity improves on Docker to make it possible to run containers in HPC environments such as super computers.  Read the full blog. 

Docker - can it be contained?

Docker - can it be contained?: Containerization technologies like Docker are designed to solve challenges associated with installing and running complex software such as bioinformatics pipelines and web servers. Docker will change the world ... maybe. While clearly powerful and enabling, the magic of Docker can also be an overpromise. To understand why, you need to understand the “The Law of Leaky Abstractions.”

Microbiome and Metagenomics Benchtop to Bioinformatics: Technical Approaches to Sequencing, DNA Extractions, and Data Analysis

Microbiome and Metagenomics Benchtop to Bioinformatics: Technical Approaches to Sequencing, DNA Extractions, and Data Analysis: Want to incorporate microbiome and metagnomics research into your lab or teaching? Sign up for the ABRF 2018 microbiome and metagnomics workshop. It may not teach you to zip-line through fire, but you will learn how to generate and manage a fire hose worth of data from microbiome projects.

Solving the Bioinformatics Singularity with Containers

Solving the Bioinformatics Singularity with Containers: ​​​​​The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated [1].” Hmmm.  That sounds like bioinformatics. Read more at Digital World Biology.

Getting Started with Infrared Photography

Getting Started with Infrared Photography: Infrared (IR) photography creates pictures in a whole new light. When I first experimented with infrared in the late 70's early 80's it was with black and white infrared film using a dark red Wratten 89b IR filter. It was okay, but not great. Digital cameras change that by opening the experience to easy experimentation to explore color and black and white.

Socializing Social Media

Socializing Social Media From communicating with friends and colleagues, to promoting business, to influencing elections, social media’s impact can be significant ... read more at Digital World Biology

Displaying peptides on MHC proteins is hard work

Displaying peptides on MHC proteins is hard work 

Lately I’ve been thinking about immunology, and not just because it is flu season, it is because Digital World Biology (DWB) is collaborating with Shoreline Community College to design a five-week bioinformatics course that will be component of their one year immuno-biotechnology certificate (1)...

Bio Databases 2018: How do they taste?

Bio Databases 2018: How do they taste?

It’s a new year and new edition of Nucleic Acids Research’s (NAR’s) Annual Database issue(link is external). It’s the 25th year for the NAR database series, the eighth for FinchTalk, and the first at the new home for Discovering Biology in a Digital World. 

Synthetic Biology: Lowering environmental impact

Synthetic Biology: Lowering environmental impact

One of the themes of the recent @synbiobeta #sbbsf17 annual meeting (Oct 4,5 2017) was the impact of synthetic biology on making new things or making old things in new ways. From cement to food, synthetic biology is causing people to rethink the way things are made. One of the most interesting ideas is the notion of using synthetic biology to manufacture materials in a way that's more friendly to the environment.  

Synbiobeta - the future is now.

Synbiobeta - the future is now.

How Big is Biotech?

How Big is Biotech?: A simple web search says biotech is really big. One estimate indicates that the industry will have $400 billion in sales in 2017 with growth to over $775 billion by 2024 [1]. Another report suggests there are over 77,000 employers [2]. That’s big, but is it real, and what you can do with this information? 



Check out the post to learn more.

BioDatabases 2017 – What’s out there?

BioDatabases 2017 – What’s out there?: It’s time for the annual blog about the annual Nucleic Acids Research (NAR) database issue. This is the 24th database issue for NAR and the seventh blog for @finchtalk. Like most years I have…

Where'd I go?

Please visit
http://scienceblogs.com/digitalbio to see @finchtalk's posts.

Bio Databases 2014

Please visit http://scienceblogs.com/digitalbio/2014/01/09/bio-databases-2014 to read the post.

Sneak Peek: Elucidating the Effects of the Deep Water Horizon Oil Spill on the Atlantic Oyster Using RNA-Sequencing Data Analysis Methods

Join us this Tuesday, May 21st at 10 AM Pacific Time / 1:00 PM Eastern Time, for an interesting webinar on the effects of the Deep Water Horizon oil spill.

Speakers:
Natalia G. Reyero, PhD. – Mississippi State University
N. Eric Olson, PhD. – PerkinElmer Sr Leader Product Development

The Deep Water Horizon oil spill exposed the commercially important Atlantic oyster to over 200 million gallons of spill-related contaminants. To study toxicity effects, we sequenced the RNA of oyster samples from before and after the spill. In this webinar, we will compare and contrast the different data analysis methodologies used to address the challenge of an organism lacking a well-annotated genome assembly. Furthermore, we will discuss how the newly generated information provided insight into underlying biological effects of oil and dispersants on Atlantic oysters during the Deep Water Horizon oil spill.

REGISTER HERE to attend.

ABRF 2013

The annual Association of Biomedical Research Facilities begins this weekend (March 2 - 5).  We [PerkinElmer] will be busy at the conference as participants and as a vendor supporting this great organization and our many customers. From client presentations to our own work we will share our latest and greatest.

Highlights:

Saturday: 3/2 "Breaking the Data Analysis Bottleneck: Solutions That Work for RNA and Exome Sequencing." Rebecca Laborde, Mayo Clinic will present on how the teams she works with use GeneSifter for they're NGS data analysis. This is part of Satellite Workshop 1: Applications of NGS.

Monday: 3/4 "Oyster Transcriptome Analysis by Next Gen Sequencing." Natalia Reyero, Genetics and Development Biology Center, NHLBI will give a presentation based on her award nominated poster (below) during the (RG5) Genomics Research Group. GeneSifter had a role in the data analysis.

Saturday and Monday Posters:

#7 "Identifying Mutations in Transcriptionally Active Regions on Genomes Using Next Generation Sequencing." Eric Olson, PerkinElmer, presents ways in which RNA-seq can be used to define transcripts to identify functional mutations in organisms that have sparsely annotated reference genomes. 

#11 "What Does It Take to Identify the Signal from the Noise in Molecular Profiling of Tumors?" Eric Olson, PerkinElmer presents ways to use RNA sequencing and bioinformatic approaches to filter the vast numbers of variants observed in DNA sequence data obtained from tumors to a manageable number that are most likely to be the drivers of tumor growth.

Award Nominee
#119 "Elucidating the Effects of the Deepwater Horizon Oil Spill on the Atlantic Oyster Using Global Transcriptome Analysis" Natalia Reyero, Genetics and Development Biology Center, NHLBI. If you are interested in learning about the aftermath of the Gulf of Mexico oil spill, you will find Natalia's work interesting. 

And that's not all. The the booth will be hopping. We will have meet the speaker opportunities on Sunday and Tuesday and as well as many demos of our GeneSifter Analysis and LIMS products.  PerkinElmer Informatics will have individuals to show new features in PerkinElmer's Electronic Laboratory Notebook and other products, and Caliper and Chemagen reps will be on hand to talk about the great things we do for sample prep.  

Check us out a Booth 522 to get schedules and see what's new.