Open Notebook Science Network

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The latest open science

Writing a NSF Grant Proposal: The Good, The Bad, and The Ugly 8 March, 2016
I think it is safe to say that most of us find applying for NSF funding a stressful and daunting experience. How could it not be? According to the 201 […]
DNA quality check 8 March, 2016
Today I continued my assessment of DNA quality for P. astreoides samples extracted earlier this winter by running them on a gel (using this protocol). […]
DNA quantitation and quality check 1 March, 2016
Today I determined DNA yield for several samples that I had not yet tested with the Qubit. Here are the results (along with previous Nanodrop results) […]
Welcome to our open science notebook! 25 February, 2016
Welcome to our open science notebook where we detail the progress of our research project on Chinese undergraduate students in U.S. institutions of hi […]
Wiley also stopped me doing my research 23 February, 2016
0000-0003-1050-6809In November, I wrote about how Elsevier wanted me to stop downloading scientific articles for my research. Today, Wiley also ordere […]
Notebook Entry 1: February 22, 2016 22 February, 2016
It has been about a month since we (the Fours of Nature: Danny Bui, Bradly Ramirez, and Nihma Salem) started in ASSURE lab again. We started the seme […]
MarineSPEED: Spatial cross-validation and variograms 22 February, 2016
As one of the downloads of the MarineSPEED dataset I’m trying to create a spatially disjoint set of subsamplings of the original dataset in order to r […]
Assessing the use of #icanhazpdf 20 February, 2016
When researchers, journalists, or any other citizen is denied access to (parts of) the scientific literature, alternative access routes will come into […]
using IPython and command line 19 February, 2016
Trying to open and work with notebook and command line by myself turned out to be more difficult than I thought. All the commands and code I used on W […]
DNA extraction 18 February, 2016
Today I completed the final round of DNA extractions from my Belize Porites samples collected in November using the Qiagen DNeasy Blood and Tissue kit […]
general 15 February, 2016
http://minasss.pblogs.gr/2016/02/open-notebook.html Bio-publications: http://www.ncbi.nlm.nih.gov/pubmed/?term=sakellakis https://scholar.google.g […]
Summary of new project 11 February, 2016
Comparing the DNA methylation pattern of oysters to see if the location the oysters are planted at changes the expression of some genes. The oysters h […]
DNA extraction 10 February, 2016
I have been moving forward with extraction of DNA from P. astreoides samples using the Qiagen DNeasy kit. On Monday/Tuesday I did 16 samples, then ano […]
MarineSPEED: broke git, lost some work 8 February, 2016
Lost a lot of time today trying to recover files that got lost due to incorrect of the bfg tool (used for removing big files in git). Finally decided […]
MarineSPEED slow data preparation and improving the UI 5 February, 2016
Distribution records Only the records for 190 species got processed last night. With another 300+ species to go performance could be improved. The bot […]
Data Management – High-throughput Sequencing Data 5 February, 2016
We’ve had a recent influx of sequencing data, which is great, but it created a bit of a backlog documenting what we’ve received. I updated our Google […]
kubu4
DNA extraction trial run #2 4 February, 2016
Yesterday I did a second trial run with the same P. astreoides samples used in the previous run (sample #s 1, 10, 97, 100; see previous post). This ti […]
Some progress on MarineSPEED.org 4 February, 2016
MarineSPEED Redownloaded all OBIS data. Prepared lab records in correct format. Prepared code for (see gist): combining all records: GBIF (hasGeoSpati […]
Hello world! 4 February, 2016
Finally took action to start my own open notebook. I’m working on marine species distribution modeling and my main tool is R so expect to see a lot of […]
Data Received – Ostrea lurida MBD-enriched BS-seq 3 February, 2016
Received the Olympia oyster, MBD-enriched BS-seq sequencing files (50bp, single read) from ZymoResearch (submitted 20151208). Here’s the sample list: […]
kubu4

Above are the 20 most recent posts in our notebooks, but there are many more!

Click here for the archives, starting at the 21st most recent post.

Example Open Notebooks

Open Source Malaria
Ant Ecology and Other Adventures
Marine bioacoustics & sustainability
Ecology of Infectious Marine Diseases [course]
chem-bla-ics
IheartAnthony’s Research
UsefulChem by the Bradley Lab

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#Oly_reciprocal_final_sampling 16s 18s actin bacterial culture BB bioanalyzer black abalone BS-seq cDNA CE CFX96 comet COX COX1 COX2 Crassostrea gigas Crassostrea virginica CT ctenidia Cycloclasticus pugetii cyclooxygenase Dg DH digestive gland DNA DNA Isolation DNA Quantification DNase DNased RNA DNazol DNA_extraction DNeasy Dungan isolates Eastern oyster EIMD electropherogram ePCR EtOH precipitation Evolution in Action Fidalgo_Bay gDNA gel gel extraction geoduck gill gonad GoTaq qPCR Probe Master Mix graphs Haliotis cracherodii Hard clam hemocyte hemolymph Immomix in-situ hybridization ipython notebook ISH jupyter notebook lake trout larvae Lean library prep liver M-MLV Malaria mantle Martha's Vineyard MBD-Seq Mercenaria mercenaria Micro PolyA Purist mRNA mRNA enrichment NanoDrop1000 O'geneRuler DNA Ladder Mix OA ocean acidification olympia oyster Opticon2 Ostrea lurida Pacific herring Pacific oyster Panopea generosa PCR PGS PGS1 PGS2 phage pics PQ prostaglandin synthase PTC-200 qPCR rad RAD-seq restriction digestion reverse transcription RLOv RLOv_DNA_helicase RNA RNA isolation RNA quantification rna-seq RNAlater Rosetta Sanger sequencing sea star Sisco siscowet SOLiD SOLiD libraries SYTO 13 SYTO13 Technology TriReagent troubleshooting Turbo DNA-free Ultrafree-DA Vibrio exposure Vibrio tubiashii Vibrio vulnificus water filters WB Whole Transcriptome Analysis Kit withering syndrome yellow perch

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