blog-di-j.blogspot.com

J's blog

Thursday, December 13, 2007. The role of bioinformatics in Open Notebook Science. At one time in my life, I must have subscribed to "what's going on in the blogosphere" email updates from Genome Technology. Recently they were promoting. A blog post about an "open notebook" bioinformatics project. From that title, you'd think that a bioinformatics person sharing their code was a rare event. It's true that raw data sharing as is still a rarity of amongst experimenters; the no-insider-information. But the t...

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Thursday, December 13, 2007. The role of bioinformatics in Open Notebook Science. At one time in my life, I must have subscribed to what's going on in the blogosphere email updates from Genome Technology. Recently they were promoting. A blog post about an open notebook bioinformatics project. From that title, you'd think that a bioinformatics person sharing their code was a rare event. It's true that raw data sharing as is still a rarity of amongst experimenters; the no-insider-information. But the t...

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2 pedro beltrao

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5 the fear of being scooped myth

6 and overcome

7 the organizational hurdle

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J's blog | blog-di-j.blogspot.com Reviews

https://blog-di-j.blogspot.com

Thursday, December 13, 2007. The role of bioinformatics in Open Notebook Science. At one time in my life, I must have subscribed to "what's going on in the blogosphere" email updates from Genome Technology. Recently they were promoting. A blog post about an "open notebook" bioinformatics project. From that title, you'd think that a bioinformatics person sharing their code was a rare event. It's true that raw data sharing as is still a rarity of amongst experimenters; the no-insider-information. But the t...

INTERNAL PAGES

blog-di-j.blogspot.com

1

J's blog: November 2007

http://blog-di-j.blogspot.com/2007_11_01_archive.html

Wednesday, November 7, 2007. My first appearance in a scientific credit list. Tim Gardner (my PI) and Michael Molla wrote a guest blog post at PLoS on how science can learn from the movie industry. At the end of a movie, the role of everyone in the movie is clearly spelled out in the movie credits, while on scientific publications you only have a list of ordered names from which to try and infer the authors' role. Excerpt from their scientific credit list. Excerpt from their scientific credit list. May b...

2

J's blog: July 2007

http://blog-di-j.blogspot.com/2007_07_01_archive.html

Tuesday, July 10, 2007. For Open Notebook Science. I recently decided to give open notebook science a try. I'm trying to catalog some basic ideas that would promote better open notebooks, with better defined as:. Dependable (i.e. small software failures won't forever zap all of your results). Here's what I've come up with so far. Please comments if you think of other tips. Use some sort of version control system (wiki, cvs, subversion). It also allows you to go back and look at previous versions. If a se...

3

J's blog: Optimized ChIP Protocols

http://blog-di-j.blogspot.com/2007/12/optimized-chip-protocols.html

Tuesday, December 4, 2007. This page contains links to a chromatin immunoprecipitation protocol optimized with factorial and response surface methods. Using three different transcription factors (two were primarily for validation). Download the new ChIP Protocols (pdf). Download the original ChIP Protocol (pdf). All raw data and experiments that went towards this protocol optimization are in my Lab Notebook. In the Chapter entitled: Towards a faster, more reliable ChIP protocol. How this blog works.

4

J's blog: J's Open Projects index

http://blog-di-j.blogspot.com/2007/10/js-projects-in-progress.html

Wednesday, October 24, 2007. J's Open Projects index. This post is an index with a one-line description of the projects I'm working on and the relevant chapter of the work in J's Lab Notebook. Read how this blog works. For more general information. 1) Cheaper, faster, better ChIP. Using statistical experimental design methods to shorten, cheapen, and optimize a Chromatin Immunoprecipitation protocol for experimentally determining transcription factor binding sites. Apr 26, 2007. How this blog works.

5

J's blog: Factorial and response surface optimization of a chromatin immunoprecipitation protocol

http://blog-di-j.blogspot.com/2007/10/factorial-and-response-surface.html

Friday, October 19, 2007. Factorial and response surface optimization of a chromatin immunoprecipitation protocol. This post describes some of my ongoing research. The raw data and all experimental details are updated daily in J's Lab Notebook. In the chapter entitled: Towards a faster, more reliable ChIP protocol. Short Version of What I'm trying to do:. In general, I think there is a lot of unnessary folklore. Longer Version of What I'm trying to do:. Validation of transcription factor targets. Ver...

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onebiglab.blogspot.com

One Big Lab: Off to ISMB 2008

http://onebiglab.blogspot.com/2008/07/off-to-ismb-2008.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Wednesday, July 16, 2008. Off to ISMB 2008. Tomorrow I'll be heading off to ISMB. No more poster tubes, little sheets of paper, curled edges, or push pins - just upload your file before you get on the plane, bring a thumb drive just in case, and you're good to go. Sure, they'd be expensive, delicate, heavy, and perhaps prone to glitches, but nothing a few years of tech i...

onebiglab.blogspot.com

One Big Lab: April 2008

http://onebiglab.blogspot.com/2008_04_01_archive.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Friday, April 18, 2008. Call for collaboration: calcium site predictions in need of validation. Time to walk the walk? If you or anyone you know is interested in collaborating with her to validate some of her predictions experimentally, please shoot me an email or respond here. Suggestions welcome, too! Monday, April 14, 2008. Emboldened by the collective fervor, I would lik...

onebiglab.blogspot.com

One Big Lab: One Big Lab has moved!

http://onebiglab.blogspot.com/2008/08/one-big-lab-has-moved.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Friday, August 22, 2008. One Big Lab has moved! I will now be posting at my all-purpose blog:. Http:/ shirleywho.wordpress.com. I was lost but now I live here". Hope you don't mind a few posts here and there on non-sciencey things, but this move was really for the best (for me, that is). Please re-subscribe, change your bookmarks, etc etc! Subscribe to: Post Comments (Atom).

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J's Page: My Life Outside of Science

http://www.jeremiahfaith.com/links.html

Below are some of the non-sciency things I like to do. 1) Travel / Digital Photography. Check out Ilaria and J's photo page. To see where I've been traveling. Lately; most trips are with my gal Ilaria Mogno. 2) Think about stuff. I spend a lot of time daydreaming about stuff. I keep an unorganized set of my half-baked ideas on J's blog. In graduate school, I was in a band that played funk and latin tunes. 4) Add knowledge to the web. My sister is a freelance graphic designer. Check out her website.

onebiglab.blogspot.com

One Big Lab: January 2008

http://onebiglab.blogspot.com/2008_01_01_archive.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Thursday, January 31, 2008. Call for letters of support for PSB proposal. Hi folks, so it's about a week until the proposal is due. So far, we have a draft. So if you would like to support this proposal and are willing to commit to participating should it get accepted, please send me an email. Labels: open science psb 09. The scooping debate continues. Posted about a scoopin...

onebiglab.blogspot.com

One Big Lab: June 2008

http://onebiglab.blogspot.com/2008_06_01_archive.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Thursday, June 19, 2008. Is there a one stop shop for (good) science videos? My advisor has recently become enamored with the idea behind SciVee. Which is essentially a place where you can view video blurbs of people's research, but is convinced that nothing short of YouTube. The Inner Life of a Cell. And this demonstration of cornstarch physics. What YouTube has going for i...

onebiglab.blogspot.com

One Big Lab: July 2008

http://onebiglab.blogspot.com/2008_07_01_archive.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Wednesday, July 16, 2008. Off to ISMB 2008. Tomorrow I'll be heading off to ISMB. No more poster tubes, little sheets of paper, curled edges, or push pins - just upload your file before you get on the plane, bring a thumb drive just in case, and you're good to go. Sure, they'd be expensive, delicate, heavy, and perhaps prone to glitches, but nothing a few years of tech i...

onebiglab.blogspot.com

One Big Lab: The future of science, gradical change, and tools for the people

http://onebiglab.blogspot.com/2008/08/future-of-science-gradical-change-and.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Friday, August 8, 2008. The future of science, gradical change, and tools for the people. That something is The Future of Science. Michael Nielsen has written about this. At length in preparation for his forthcoming book of the same name, with a lively discussion in the comments following. At BioBarCamp. This past weekend (many thanks to John Cumbers and Attila Csordas.

onebiglab.blogspot.com

One Big Lab: Got platelets?

http://onebiglab.blogspot.com/2008/08/got-platelets.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Thursday, August 21, 2008. See below for more information. Kathryn Meacham, Patient ID: 754592. Friends and Family,. We are writing because we hope you can help secure or donate blood platelets in the Houston area for our sister/cousin Kathryn (Katie) Meacham. Katie is presently undergoing treatment at MD Anderson for a very aggressive strain of Hodgkin's Lymphoma! Wendy, Al...

onebiglab.blogspot.com

One Big Lab: August 2008

http://onebiglab.blogspot.com/2008_08_01_archive.html

One small world = One Big Lab. Exploring the potential behind open science, open access, and open exchange of more than just ideas. Friday, August 22, 2008. One Big Lab has moved! I will now be posting at my all-purpose blog:. Http:/ shirleywho.wordpress.com. I was lost but now I live here". Hope you don't mind a few posts here and there on non-sciencey things, but this move was really for the best (for me, that is). Please re-subscribe, change your bookmarks, etc etc! Thursday, August 21, 2008. If you k...

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blog-di-j.blogspot.com

J's blog

Thursday, December 13, 2007. The role of bioinformatics in Open Notebook Science. At one time in my life, I must have subscribed to "what's going on in the blogosphere" email updates from Genome Technology. Recently they were promoting. A blog post about an "open notebook" bioinformatics project. From that title, you'd think that a bioinformatics person sharing their code was a rare event. It's true that raw data sharing as is still a rarity of amongst experimenters; the no-insider-information. But the t...

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Diabetes | Diabetes Information | Diabetes Risks, Symptoms,Causes, Diagnosis,and Treatment

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