Linear regime-dog-110310
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The document contains graphs showing linear regression lines fitted to scatter plots of data points, along with the equations for the linear regression lines and R-squared values. Multiple linear regressions are shown using different x-ranges for the data points.
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“Open source” is the act of providing software, technology, or process for free and inviting amendments and derivation. Open sourcing philosophy has emerged primarily in the software industry, but over the past decade the open movement has risen from an unconventional concept to an emerging approach now applied to many other fields including communication, STEM, art, and many others. When money is involved, open policies are seen as unfavorable and have been largely disregarded. Current resistance to open access is not well understood but may be stem from questions of profitability or fears of losing intellectual property. In this open discussion, which we want the audience to participate in, we hope to present the possibility of using open practices to build a successful business model. What if providing open access could make a company more profitable? What if transparency brought more customers? What’s more, what if open practices could add a new dimension to corporate social responsibility? We present the idea that openness in a corporation would actually be extremely beneficial to businesses and organizations alike, and could drive profitability and induce trust while minimizing corruption and ensuring corporate, societal, and fiscal responsibility.
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Deuterium is present in all naturally occurring water, and accounts for 1 in 6420 hydrogen atoms. Seemingly insignificant, that ratio is actually quite impactful in life sciences. Pure deuterium oxide (heavy water) has been found to be toxic to eucharyotic organsims, and has been found to be inhibitory in smaller doses. Here I present results that demonstrate that in even smaller doses the concentration of deuterium has a dramatic effect on life processes. I also show that at the molecular level, deuterium has a stabilizing effect. By simply changing the properties of the solvent, there can be dramatic effects that impact a variety of experiments.
For the entire story, please refer to my dissertation: https://docs.google.com/document/d/1p9-qqF8oUcwNGJjZG3CoKL2xvIhbqKCFQ7_faegNPIU/edit?usp=sharing
Open Notebook Science: Research in Real-Time
Presented on 2/15/13 for Student Research Day at UNM. Scientific information is published in peer reviewed journals as a complete account. Unfortunately there is nothing complete about the process. Frequently intermediate and supplementary experimental data is excluded, methods are not nearly detailed enough, and results are manipulated for appearance. Open notebook science aims to be a complete account of the scientific process: from ideas and planning, to experimental setup and protocol design, all the way through data interpretation and commentary. Here I
talk about tools to create and support an open notebook, effective use of the medium, and how social interaction creates a community using examples from my own open notebook for research.
Open Notebook Science - SACNAS Poster
Here I present some of the best tools for open notebook science and a brief discourse as to what open notebook science is, why it is important, and how it will permeate scientific culture.
My abstract from SACNAS:
Open Notebook Science - UNM Biomed Symposium Edition
Scientific information is published in peer reviewed journals as a complete account. Unfortunately there is nothing complete about the process. Frequently intermediate and supplementary experimental data is excluded, methods are not nearly detailed enough, and results are manipulated for appearance. Open notebook science aims to be a complete account of the scientific process: from ideas and planning, to experimental setup and protocol design, all the way through data interpretation and commentary. Here I talk about tools to create and support an open notebook, effective use of the medium, and how social interaction creates a community using examples from my own open notebook for research.
Open Notebook Science: Research in Real-Time
A presentation I gave to students at the New Mexico Graduate and Professional Student Conference. Open science is the future of science, and open notebook science is the future of how scientific information is accessed and propagated. Here I present examples from my notebook and from a case study of an open notebook community (Physics 308L Junior Lab).
Cyber Infrastructure Day
Using Web 2.0 technologies like YouTube, Google Docs, Flickr, Dropbox, and blogs, scientists can now publish and share data, protocols, results, and notes in near real-time with students, colleagues and the public. These technologies allow for easy archiving, collaboration, and promotion of research materials through embedding, linking, and aggregating content across different online platforms and mobile devices. The KochLab highlights how it leverages various free cloud services and apps to streamline data recording, analysis, documentation and distribution.
Shotgun DNA Mapping for IGERT
Shotgun DNA mapping involves three steps: 1) digesting genomic DNA into fragments, 2) unzipping the fragments and recording the force curves, and 3) comparing the experimental force curves to a library of simulated curves to match fragments to locations in the genome. The document discusses how unzipping DNA can detect proteins bound to it based on deviations in the force curve from naked DNA. It presents results matching an experimental plasmid unzipping force curve only to the corresponding simulated plasmid curve within a library simulating an entire yeast genome.
Mechanical Properties of Biological Nanocomposites
The document discusses the mechanical principles of biological nanocomposites. It begins by introducing the speakers and topics to be covered. It then examines the nanostructure of biological materials like bone and how they achieve excellent mechanical properties through hierarchy and interactions between proteins and mineral plates. The focus is on understanding these factors and applying them to synthesize robust synthetic materials through biomimicking. It covers concepts in fracture mechanics, plasticity, toughness and how nature improves strength. Examples of different biological materials and their hierarchical structure-function relationships are provided.
BPS 2010 Poster Presentation: Shotgun DNA Mapping with Yeast
This is my poster presentation from the annual Biophysical Society Meeting in San Francisco, CA. I detail the current progress made in Shotgun DNA mapping and include an aside about open notebook science and my scientific life on the internet.
KochLab Summary
Here is a summary by Andy Maloney and myself. This describes what we basically do in the lab and why we have so much fun doing it. This presentation was a blast to make and I look forward to doing many more.
Credit: The song is "Missing You" by Trash80 from the album Icarus. It can be downloaded from 8bitpeoples.com.
Protein-DNA Mapping using an AFM
The document discusses using atomic force microscopy (AFM) to map protein-DNA interactions. It outlines how AFM chips can be fabricated through photolithography to include nanochannels. The chips allow rapid detection of protein-bound DNA, which has applications for studying gene expression, DNA restriction, and DNA mutations. Questions from researchers using the technique are also addressed.
Proposal for Protein-DNA Mapping using AFM for Lab on a Chip
This was a report written for a class I am taking in conjunction with Ken Seal, John Montoya, and Laura Pawlikowski. We discuss functionalizing an AFM tip with antibodies for protein detection. Conceptually, proteins bound to DNA can be flowed down a nanochannel and can be detected by an AFM tip in the channel. The detection will be based on the interaction between antibodies and their antigens (the proteins). This proposal details everything we imagined. We presented on this topic as well.
Candidacy Exam Final Version
This is a presentation I gave for my Candidacy for PhD. I present on the possibilities of probing protein-DNA interactions using Optical Tweezers. I discuss simulating force curves from optical tweezers, background information, and the molecular biological preparations involved. Finally I conclude with future applications of the technique that range from analysis of alternative splicing, transcriptional studies, and telomere mapping.
Practice Candidacy Exam
This document provides an overview of shotgun DNA mapping using single molecule DNA analysis techniques. It discusses digesting genomic DNA into random fragments, constructing DNA tethers for optical tweezers unzipping, simulating unzipping profiles to create a library for comparison to experimental data, and potential applications for studying chromatin structure, transcription, and telomeres. The goal is to map DNA sequences to their genomic locations in order to better understand protein-DNA interactions and gene expression.
Practice Candidacy Exam
This document provides an overview of shotgun DNA mapping using single molecule DNA analysis techniques. It discusses digesting genomic DNA into random fragments, constructing DNA tethers for optical tweezers unzipping, simulating unzipping profiles to create a library for comparison to experimental data, and potential applications for studying chromatin structure, transcription, and telomeres. The goal is to map DNA sequences to their genomic locations in order to better understand protein-DNA interactions and gene expression at the single molecule level.
Thorough Intro To SDM For Osley Lab (82109)
I made this presentation to show some collaborators whose lab I worked in last semester. In it I discuss the past, present, and future of Shotgun DNA Mapping and all that it contains.
Gravitational Lensing and Stuff
My girlfriend made a presentation summarizing her REU experience. It is about gravitational lensing and the work she did trying to distinguish characteristics of lenses caused by galactic clusters. That is the best summary I can give.
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Linear regime-dog-110310
- 1. y = 0.7374x - 1869.2 R² = 0.9895 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.45E+03 2.50E+03 2.55E+03 2.60E+03 2.65E+03 Series1 Linear (Series1) -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 2.50E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm)
- 2. -2.50E+02 -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 2.50E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm) y = 0.6687x - 1688.2 R² = 0.9472 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.40E+03 2.45E+03 2.50E+03 2.55E+03 2.60E+03 Series1 Linear (Series1)
- 3. y = 0.7248x - 1965.5 R² = 0.9972 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.60E+03 2.65E+03 2.70E+03 2.75E+03 2.80E+03 Series1 Linear (Series1) -2.50E+02 -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 2.50E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm)
- 4. y = 0.5531x - 1485.7 R² = 0.9858 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.55E+032.60E+032.65E+032.70E+032.75E+032.80E+03 Series1 Linear (Series1) -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm)
- 5. y = 0.5385x - 1418 R² = 0.9948 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.50E+032.55E+032.60E+032.65E+032.70E+032.75E+03 Series1 Linear (Series1) -2.50E+02 -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm)
- 6. y = 0.7077x - 1824.7 R² = 0.992 -6.00E+01 -4.00E+01 -2.00E+01 0.00E+00 2.00E+01 4.00E+01 6.00E+01 2.50E+03 2.55E+03 2.60E+03 2.65E+03 2.70E+03 Series1 Linear (Series1) -2.50E+02 -2.00E+02 -1.50E+02 -1.00E+02 -5.00E+01 0.00E+00 5.00E+01 1.00E+02 1.50E+02 2.00E+02 2.50E+02 0.00E+001.00E+032.00E+033.00E+034.00E+035.00E+036.00E+03 X (nm) X (nm)