User:AM Bentley/Notebook/Biology 210 at AU

February 21 2016 - '''INSTRUCTIONS TO ANALYZE AND RECORD YOUR 16S SEQUENCING DATA'''

1. Follow this link – this link will show the sequencing reactions from the forward primer https://clims3.genewiz.com/links.aspx?oId=Y0pURRzK0Ks=&ref=00

When prompted, login with: Username – meg@american.edu Password – Monster1

2. Find your sequences that correspond to a MB# tube label. The MB# tube label is indicated on the log sheet that you filled out when you ran your PCR products. Once you find your sequences, select to “View” the SEQ File associated with your tubes. This will bring up a new window with the sequence of your 16S PCR product. The red circle in the screen shot below indicates the link to view the SEQ file for reaction MB05.

3. Copy and paste your sequences into your lab notebook at OWW (Note: you should copy and paste the entire sequence, but when you do a search for its match in step 5, exclude all the NNNNNNNs at the beginning or end. N means the nucleotide was difficult to read)

4. Navigate to BLAST at http://blast.ncbi.nlm.nih.gov/Blast.cgi

5. Select “nucleotide blast” search and paste in your sequence into the box at the top of the screen and hit BLAST at the bottom of the page. You may have to wait as the website queries the database – this may take up to 30 seconds!

Your results will look something like the screen shot below! The series of red lines indicates a ‘match’ for your sequence. If you scroll down below the graphic summary, you will find descriptions of the matches. Select the highest match (which is at the top of the list) and follow this link. When you verify the genus species of your bacteria by 16S sequence analysis, then go back to the microbiology lab and confirm that your colony morphology, gram stain and bacterial cell shape are correct.

Here is the PDF of the above directions that includes screen shots! Note, the link is updated for the 2016 semester, so make sure you use the link in the directions above! File:Directions for 16S Sequencing Analysis.pdf Love, Dr. Bentley

January 28, 2016! To make tables beautiful in your OWW lab notebook - follow this link! http://excel2wiki.net/index.php

P1248-1VL	Anti-phospho-ATF-2 (pSer490/pSer498) antibody produced in rabbit	affinity isolated antibody, buffered aqueous glycerol solution
P1249-200UL	Anti-Potassium Channel KCa1 slobeta4 Auxilliary Subunit antibody produced in rabbit	affinity isolated antibody, lyophilized powder
P1249-50UL	Anti-Potassium Channel KCa1 slobeta4 Auxilliary Subunit antibody produced in rabbit	affinity isolated antibody, lyophilized powder
P1369-100UG	Anti-PMCA3 antibody produced in rabbit	~1 mg/mL, affinity isolated antibody, buffered aqueous solution
P1373-1VL	Anti-Potassium Channel Kv2.2 Subunit (Voltage Gated) antibody produced in rabbit	affinity isolated antibody, buffered aqueous glycerol solution
P1495-200UL	Anti-Phosphatidylserine Receptor antibody produced in rabbit	1-1.5 mg/mL, affinity isolated antibody, buffered aqueous solution

== Making letters a different color??? ==

January 11 2016 - It's a new semester folks! Let's jump right in with a little OWW fun! MB

February 24 2015 - '''INSTRUCTIONS TO ANALYZE AND RECORD YOUR 16S SEQUENCING DATA'''

1. Follow this link – this link will show the sequencing reactions from the forward primer https://clims3.genewiz.com/links.aspx?oId=4p6LZ4Isjwk=&ref=00 The reactions for the reverse reaction can be found at... https://clims3.genewiz.com/links.aspx?oId=HMu/TLANFLc=&ref=00

When prompted, login with: Username – meg@american.edu Password – Monster1

2. Find your sequences that correspond to a MB# tube label. Once you find your sequences, select to “View” the SEQ File associated with your tubes. This will bring up a new window with the sequence of your 16S PCR product. The red circle in the screen shot below indicates the link to view the SEQ file for reaction MB05.

3. Copy and paste your sequences into your lab notebook at OWW

4. Navigate to BLAST at http://blast.ncbi.nlm.nih.gov/Blast.cgi

5. Select “nucleotide blast” search and paste in your sequence into the box at the top of the screen and hit BLAST at the bottom of the page. You may have to wait as the website queries the database – this may take up to 30 seconds!

Your results will look something like the screen shot below! The series of red lines indicates a ‘match’ for your sequence. If you scroll down below the graphic summary, you will find descriptions of the matches. Select the highest match (which is at the top of the list) and follow this link. When you verify the genus species of your bacteria by 16S sequence anlysis, then go back to the microbiology lab and confirm that your colony morphology, gram stain and bacterial cell shape are correct.

Here is the PDF of the above directions that includes screen shots! File:Directions for 16S Sequencing Analysis.pdf Love, Dr. Bentley

January 28 2015 A PDF of the Lab Notebook Rubric that all of your TAs will be using!

File:Lab Notebok Rubric PDF.pdf

Also, MB was having issues downloading/opening the files below so I made them into PDFs and posted those below. Once you click on the link, it brings you to the file's page. Keep following the link to open the PDF in a screen.

File:OWW tips AP.pdf File:Openwetware how to upload photos AP.pdf

January 26 2015

File 1: How to upload pictures. file 2: OWW tips. Click and download file!

Media:Pedersen_oww_picture_tutorial.docx‎
Media:OWW_tips_.docx‎

AP

January 14 2015 Biology 210 is the best thing ever! January 14 2015 Convert an excel table to wiki at http://excel2wiki.net/ Here is the OWW page that is most up to date on the conversion tools -- join the conversation! http://openwetware.org/wiki/Converting_documents_to_mediawiki_markup

Organism	Size	Reproduction?
chlamy	10	iso
gonium	50	oo
volvox	213	oo

January 12 2014: All Spring 2015 Biology 210 students! Make sure your bring your OWW username (not your AU username) to your first lab! In lab, we will go over some basics of OWW. It's going to be a great semester!

June 9 2014: Just added a section for Summer 2014. Once you request a username and password from OWW, send that to your TA and then we can assign you a lab notebook!

February 2 2014: We can finally add pictures! To do this follow the directions... 1. First, make sure when you are adding text along with pictures, type in the text and save it. Then upload photos and add those within the previously saved text. 2. To add photos (or anything other than text) select 'upload file' on the toolbox on the left hand menu. 3. Follow the prompts to upload a file. You should save images as .png files with the lowest resolution possible to make them easily viewable. 4. Once you upload the image, copy the image name at the top of the image file. 5. Copy and paste it into your lab notebook with square brackets before and after. I have included a picture of my dog here as an example. Remember, you can look at the code that has allowed me to post this image by going to the 'edit' tab at the top.

January 29 2014: Please note students that we are still having trouble with file uploads. This is the website which is trying to solve the problem, so I have no control over this glitch. What I recommend is saving all of your images in some annotated way to a word document or a powerpoint or to microsoft paint. This way, you will have them all in one tidy place and you can upload once the problem is resolved. Be patient and I will let you all know once we are back up! MB

January 24 2014 i am testing to see whether i can enter something into this page and it populates every TA notebook in other sections? MB

we now have a shared TA notebook -- that means TAs should sign anything that they enter into the lab notebook MB

January 23 2014: Today in lab you should make sure that you enter something into you lab notebook to make sure that you are set up properly and that you know how to do this. Please follow the standard we are establishing now which is beginning with the date of entry. Always bold the date Then enter data, images and tables. Then sign your entry with your initials. Also, the most recent entry should be at the top. So every time you enter something into OWW, begin at the top. Beginning next week, I will have expectations that you are adding transect data frequently! MB

January 21,2014: Folks! I am trying to figure out a set of instructions for uploading images. I know that some of you have gotten "file appears to be empty" messages. I am working on it today while the snow falls! MB

January 12, 2014: Biology 210 – Organismal Biology How to keep a complete lab notebook

The Importance of the Laboratory Notebook:

Keeping a good lab notebook is a vital part of science. Before the digital age, accurate record keeping was the only mechanism that was in place for advancing science. Long before each of us started school, a scientist was at his/her bench spending hours writing down how he/she did an experiment and what was witnessed. It is only this detail that allowed us to understand chromosomes, describe organelles, or develop vaccines. The whole point of the laboratory notebook is to: (1) write down exactly who did an experiment, when it was done, and the methods that were used (2) allow information to be validated and sustainable (important for legal issues like patents too!) (3) enable someone else to replicate the experiment at a later date

Lab Notebook Guidelines:

Similar to the requirements that are set forth by industry (and government research institutes like NIH and FDA), laboratory notebooks should be:

   (1)  hardback bound notebooks or electronic format
   (2)  documentation of original thought, even if that thought is a mistake. 
   (3)  If you make corrections, simply cross out old information and write the corrected statement next to it
   (4)  as complete as possible.  
   (5)  You may write things down on scraps of paper and transfer to the notebook later, but don’t rely on your memory for the details

Organization of the notebook:

Your notebook should be so clear, complete, and concise that anyone could pick up your notebook and understand what you have written. Your notebook should contain the following format.

   (1)  Introduction (general description of what you are doing)
   (2)  Purpose (general description of why you are doing an experiment)
   (3)  Materials and Methods (detailed description of how you did an experiment)
   (4)  Data and Observations
   (5)  Conclusion (and ideas for future experiments)

Introduction: Your introduction should have the following: a) the title of the experiment - keep your title descriptive yet concise b) the date (make sure you include the year, not just the month and day) Purpose: The purpose should be a statement of what the problem that you are studying is. Be short and to the point. It is in this section that you will want to include a hypothesis or prediction. (Remember! Your hypothesis does not need to be correct to be doing good science.)

Materials and Methods: This section explains what you did in the experiment. You should use simple, direct statements that may be written in bullets, numerically, or essay format. As long as the detail is there, it doesn’t matter what format you use. I can’t state enough that you need to be very complete in this area. No detail is too small to be included. A fellow scientist (and group member) should be able to repeat your experiment based on these details.

Observations and Data The observations and data should be: (1) Recorded honestly!!! Remember, sometimes unexpected findings are what lead us to the best scientific advances. Everything has some meaning, even if it doesn’t make sense at the time (2) Recorded as you go along in the notebook. Don’t trust your memory. You will forget the little details. You can make notes and then transfer to a lab notebook or openwetware. (3) Recorded as completely as possible. You don’t need to interpret the data in this section, for you will do that in the next section (4) Recorded in an easy to read format. You can draw graphs or write tables in this section to illustrate your data in a more user-friendly way

Conclusions Your conclusions should be based on your data. Therefore, they may not agree with your purpose or hypothesis, and this is O.K. Explain whether your data supported or refuted your hypothesis. You may want to include any ideas that this experiment generated before you forget them. This is where you can make suggestions to improve your experimental design and say what you plan to do next (e.g., “next time I may want to harvest a sample from 5 inches below the surface because I think that the temperature at the surface is too cold to get a diversity of protists…”)

Remember, unless your data is recorded in a notebook in an accurate and precise fashion, it can never be used to advance science!!!