tag:blogger.com,1999:blog-32189326456254156042024-03-19T00:54:52.331-07:00FinchTalkFinches continually evolve and so does science. Follow the conversation to learn how data impacts our world view.Sandra Porterhttp://www.blogger.com/profile/09209950581908760880noreply@blogger.comBlogger173125tag:blogger.com,1999:blog-3218932645625415604.post-60015888425499291152019-03-05T08:22:00.001-08:002019-03-05T08:22:36.602-08:00ABRF 2019: Immuno-biotechnology and bioinformatics in Community CollegesABRF 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 MoreTodd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-68542258908175301302019-01-25T06:41:00.001-08:002019-01-25T06:41:52.013-08:00Bio Databases 2019: ImmunologyBio 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.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-62406239408368545632019-01-17T06:36:00.001-08:002019-01-17T06:36:58.168-08:00How 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 MoreTodd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-31457982276054167732018-10-31T06:53:00.001-07:002018-10-31T06:53:05.467-07:00Turning into pumpkins with Molecule WorldTurning 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-13291053725581378342018-04-17T14:56:00.001-07:002018-04-17T14:56:10.752-07:00Singularity: 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-52229828562086101912018-03-27T05:55:00.001-07:002018-03-27T05:55:25.899-07:00Docker - 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-22130706450802127682018-03-22T10:17:00.001-07:002018-03-22T10:17:34.235-07:00Microbiome and Metagenomics Benchtop to Bioinformatics: Technical Approaches to Sequencing, DNA Extractions, and Data AnalysisMicrobiome 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-48715002256498727912018-03-14T06:25:00.001-07:002018-03-14T06:25:29.720-07:00Solving the Bioinformatics Singularity with ContainersSolving 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.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-6559735649108117412018-02-27T16:47:00.001-08:002018-02-27T16:48:28.565-08:00Getting Started with Infrared PhotographyGetting 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-77560548882672781392018-02-22T10:47:00.001-08:002018-02-22T10:48:41.007-08:00Socializing Social MediaSocializing 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 BiologyTodd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-59810856066145661532018-02-08T11:14:00.001-08:002018-02-08T11:17:21.577-08:00Displaying peptides on MHC proteins is hard workDisplaying 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)...
Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-66603340185496245962018-01-19T11:18:00.000-08:002018-02-08T11:19:33.381-08:00Bio 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.
Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-39302819229814404342017-10-28T13:40:00.001-07:002017-10-28T13:41:48.360-07:00Synthetic Biology: Lowering environmental impactSynthetic 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 Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-59757659589580557152017-10-28T13:21:00.001-07:002017-10-28T13:21:57.839-07:00Synbiobeta - the future is now.Synbiobeta - the future is now.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-13635007985986710132017-08-16T11:12:00.001-07:002017-08-16T11:12:58.383-07:00How 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.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-41836572226514817312017-01-12T17:12:00.001-08:002017-01-12T17:12:35.095-08:00BioDatabases 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…Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-41805553876208802152014-01-27T14:09:00.003-08:002016-03-31T16:39:41.463-07:00Where'd I go?Please visit
http://scienceblogs.com/digitalbio to see @finchtalk's posts.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-75694399833643673092014-01-10T09:29:00.005-08:002014-01-10T09:30:35.573-08:00Bio Databases 2014Please visit http://scienceblogs.com/digitalbio/2014/01/09/bio-databases-2014 to read the post.Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-51623297313221074872013-05-12T12:32:00.000-07:002013-05-12T12:32:14.111-07:00Sneak Peek: Elucidating the Effects of the Deep Water Horizon Oil Spill on the Atlantic Oyster Using RNA-Sequencing Data Analysis MethodsJoin 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 DevelopmentThe Deep Water Horizon oil spill exposed the commercially important Atlantic oyster to over 200 million gallons of Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-79932916230527092762013-02-28T13:58:00.002-08:002013-03-11T17:33:28.191-07:00ABRF 2013The 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: Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-72797583159297079532013-02-09T15:58:00.001-08:002013-02-09T15:59:11.831-08:00Genomics Genealogy Evolves
The ways massively parallel DNA sequencing can be used measure biological systems is only limited by imagination. In science, imagination is an abundant resource.
The November 2012 edition of Nature Biotechnology (NBT) focused on advances in DNA sequencing. It included a review by Jay Schendure and Eriz Lieberman Aiden entitled “The Expanding Scope of DNA Sequencing [1],” in which the authors Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-20392109842933956012013-01-27T13:23:00.000-08:002013-01-27T13:23:50.084-08:00Sneak Peek: Identifying Mutations in Expressed Regions of Genomes Using NGS Join us Wednesday, January 30th at 1 PM (EST), 10 AM (PST) to learn how to use NGS to identify mutations in expressed regions of genomes.
Abstract:The pace at which genome references are being generated for plants and animal species is rapidly increasing with Next Generation Sequencing technologies. While this is a major step forward for researchers studying species that previously did not have Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-66219425968891372242013-01-17T06:16:00.000-08:002013-01-17T06:16:03.403-08:00Bio Databases 2013 I seem to have committed to an annual ritual of summarizing the Nucleic Acids Research (NAR) Database Issue [1]. I do this because it is important to understand and emphasize the increasing role of data analysis in modern biology and remind us about the challenges that persist in turning data into knowledge.
Sometimes I hear individuals say they are building a database of all Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-67896734388789726152012-12-04T07:55:00.001-08:002012-12-04T07:55:53.251-08:00Commonly Rare
Rare is the new common. The final month of the year is always a good time to review progress and think about what's next. In genetics, massively parallel next generation sequencing (NGS) technologies have been a dominating theme, and for good reason.
Unlike the previous high-throughput genetic analysis technologies (Sanger sequencing and microarrays), NGS allows us to explore genomes in Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0tag:blogger.com,1999:blog-3218932645625415604.post-71835140989789569482012-08-05T13:20:00.000-07:002012-08-05T13:20:40.155-07:00Remembering Chris AbajianChris Abajian was a change catalyst. Using a biochemical analogy, passion, creativity, and intellect were his catalytic triad. Together, with Joe Slagel, Chris, and I started Geospiza in 1997. Sadly, Chris recently died in a hiking accident (7/30/12). In remembrance, I'll share a few stories from our times together.
I met Chris during my Postdoc in Leroy Hood's laboratory in Todd Smithhttp://www.blogger.com/profile/06957762010550357265noreply@blogger.com0