eamag/protocols-with-steps huggingface dataset:
TITLE: Set Up Biodata Resource Inventory in Google Colab
AUTHORS: Kenneth Schackart

[DESCRIPTION]
This protocol will guide you on how to get everything in place to update the Biodata Resource Inventory.

This protocol describes how to setup Google Colab, connect your Google Drive, and clone the repository.

Some of the information here came from the following article: https://medium.com/analytics-vidhya/how-to-use-google-colab-with-github-via-google-drive-68efb23a42d

[STEPS]
SECTION: Prepare Google Drive
1. In your Google Drive home directory, create a new folder called GitHub.

Inside the GitHub folder, create another folder called biodata_resource_inventory.
SECTION: Connect Colab to Drive
2. Go to Google Colab.

If you need to change the account you are using, close the pop up by clicking Cancel at the bottom right. Change your Google account by clicking the icon at the top right.
SECTION: Connect Colab to Drive
3. A menu will pop up. At the bottom right, select: "New Notebook"
SECTION: Connect Colab to Drive
4. In the cell, paste or type the following:

 
Click the "run" button to the left of the cell or run with ctrl+enter

You will be prompted to allow Google Colab to access your Drive, say yes.
 

SECTION: Connect Colab to Drive
5. Create a new code chunk by clicking "+ Code" under the top-left banner. In that cell paste or type the following, then run:

 

This has changed your current directory to GitHub.
 

SECTION: Create GitHub Access Token
6. Go to GitHub.

Go to Settings, navigate to Developer settings and click on Personal access tokens.
SECTION: Create GitHub Access Token
7. Click Generate new token button on the top right corner of the page.

SECTION: Create GitHub Access Token
8. Click the repo checkbox under Select scopes.
SECTION: Create GitHub Access Token
9. Click the Generate token button at the bottom of the page.
SECTION: Create GitHub Access Token
10. You have now created a new access token. Copy the token to your clipboard. Do not close this page yet.

 

SECTION: Clone the Repository
11. Go back to your Colab Notebook, create a new Code cell, and enter the following, pasting your access token into the quotations, then run:

 

SECTION: Clone the Repository
12. Create a new code cell and paste or type the following, then run:
 

And cd into the repository:

 

Note: During development, the main branch is mostly empty. To switch to the development branch run the following in a code cell:

 

Congrats! You now have linked Google Colab to GitHub for access to their API, and you have cloned the repository into your Google Drive. You can now close the page with your access token.
SECTION: Running the pipelines
13. You can now access all the files in the repository via traditional Google Drive.
SECTION: Running the pipelines
14. You will find two notebooks in the repository:
running_pipeline.ipynb: This allows reproduction of the original results
updating_inventory.ipynb: This guides you to update the inventory

Each notebook provides instructions on their respective process, and includes already filled-in code chunks. So you should have to do little more work to run those pipelines.
TITLE: Guardian Botanicals Blood Balance Australia 2022: Does It Work? My Latest Report
AUTHORS: health  

[DESCRIPTION]
Guardian Botanicals Blood Balance Australia, as I might want to think, is a marvelous thing! This pill will assist your body with fixing itself. Here, you trust in your judgment to successfully pick.

It will help you in living a superior and seriously enchanting life. This is the best treatment for hypertension and diabetes. It's all-ordinary and non-hurtful! It furthermore attempts to address the essential justification for your difficulty!

The Guardian Blood Balance Formula has transcendent outcomes and leaves you puzzled at how it affects you! Do this activity before the arrangement ends. This is the most effective way of treating your hypertension and diabetes.

Track down the proper ways of chipping away at your prosperity and solicitation this blood balance formula. On the off chance that you don't come by great results from using this pill, you could request a rebate. Taking into account that, this thing goes with a 100 percent unlimited guarantee. So the thing could you say you are holding on for? Get your container of Guardian Botanicals Blood Balance right now!!

[STEPS]
TITLE: Dawatek COVID protocol
AUTHORS:  Leela Raavi,  Davina Moossazadeh, Isaac Chadri

[STEPS]
?. Use oral saliva swab kit  to obtain minimum   of saliva, maximum
1 mL
2 mL
?. Add   of gold nanoparticles and   of saliva into 5mL-eppendorf tube. Mix using vortex mixer for .
1 mL
1 mL
?. Place tube into sample holder of Raman spectrometer and turn on then press scan.
?. Results will display within seconds
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>A protocol to encapsulate plant protoplasts using a PDMS microfluidic chip. Work was funded by Cambridge Synthetic Biology Strategic Research Initative (SRI) SynBio Fund.</p>
<p>http://www.synbio.cam.ac.uk/synbiofund</p>

[BEFORE_START]
<p>Prepare protoplasts.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Protocol collection: Phage DNA isolation and chemical analysis
AUTHORS: Adair  Borges

[DESCRIPTION]
Bacteriophages (phages) are viruses that infect bacteria. Some phages chemically modify their genomes to protect them from degradation by bacterial immune systems. We can detect phage genome modifications with mass spectrometry (MS) and high-performance liquid chromatography (HPLC) of phage nucleosides. This collection contains protocols for the entire process: phage growth and concentration, DNA extraction, and chemical analysis of phage nucleosides. We optimized these protocols using E. coli phage T4 and B. subtilis phage SPO1.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><strong>Background</strong></p>
<p>Atrial fibrillation (AF) is a major risk of ischemic stroke unless treated with anticoagulant. Detection of AF can be difficult because AF is often paroxysmal and asymptomatic. The aim of this study is to develop a screening model for detecting AF in a primary health care setting and to start oral anticoagulant therapy in high risk patients to prevent stroke.</p>
<p><strong>Methods and Findings</strong></p>
<p>A cross-sectional study. All of 70- to 74-year-old individuals registered at a single primary health care centre in Stockholm were invited to AF screening upon visiting the centre during a ten-month period. Those who did not have contact with the centre during this period were invited to participate by letter. Intermittent ECG recording, 30 seconds twice a day, using a hand-held Zenicor device over a 2-week period, was offered to participants without AF. Oral anticoagulant therapy was offered to patients with newly detected AF.</p>
<p>A total number of 324 (78.1%) out of 415 identified persons participated in the study. The mean age of the participants was 72 years, 52.2% were female and the median CHA2DS2-VASc was 3. Previously diagnosed AF was found in 34 (8.2%) persons in the target population. Among participants without previously known AF, 16 (5.5%) cases of new AF were detected. The final AF prevalence in the target population was 12%. Initiation of oral anticoagulant therapy was successful 88% of patients with newly detected AF.</p>
<p><strong>Conclusions</strong></p>
<p>The AF screening project showed a high participation rate and yielded a high rate of newly discovered AF of which 88% were able to be treated with oral anticoagulant.</p>

[STEPS]
?. 
?. 
?. 
?.
TITLE: Protocols for the genome assembly and annotation of the Bungarus multicinctus
AUTHORS: Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang

[DESCRIPTION]
Background: Snakes are one of the most important wildlife resources and are widely distributed. Bungarus multicinctus is a highly venomous snake and is distributed in central and southern China. In recent years, venomous snake bites have gradually increased. Genomic resources are significant for understanding the evolution of a specie and the molecular mechanisms of toxin production.


Find: Here we present a highly- continuous genome assembly of B. multicinctus. The genome size of B. multicinctus is 1.51Gb. The maximal length of scaffold is 39.68M and the N50 length is 6.55M. The B. multicinctus has a GC content of 37.8%.




[STEPS]
TITLE: 10x Protocols: Visium Fresh Frozen Methanol Fixation, H&amp;E Staining &amp; Imaging-- University of Minnesota TMCs (CG000160 Rev C)
AUTHORS: 10x Genomics, Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression on Fresh Frozen / OCT samples. Completed without CytAssist component. 

Version of protocol used: 
   10x protocol CG000160 Revision C -- Methanol Fixation, H&E staining, and imaging 

Additional protocols added for guidance:
    10x protocol for imaging guidelines (CG000241, Rev D)
    10x protocol for tissue preparation guidelines (CG000240, Rev D)

Note: These protocols may not be the current version offered by 10x Genomics but were used to produce the specific datasets connected to them. Please review the 10x Genomics support website for the most recent versions of the protocols prior to starting your experiment. 

[STEPS]
1. 10x protocol CG000160, Rev C (Fixation/H&E etc):
  

2. Additional Protocols/Resources
  CG000241, Rev D
  CG000240, Rev D
https://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen
TITLE: Hamstring muscle architecture assessed sonographically using wide field of view: a reliability study
AUTHORS: Kevin Cronin

[DESCRIPTION]
Hamstring injuries are very common in field sports. Muscle architecture has been suggested as a risk factor for hamstring strain injury. Various medical imaging techniques (Magnetic Resonance Imaging and Ultrasound) have been developed to assess muscle architecture. Ultrasound is often used to assess in vivo hamstring muscle architecture. The architecture of the hamstring muscles often extends outside the ultrasounds field of view. Previous ultrasound techniques used often generate questionable results. This study aims to describe the reliability of large field of view ultrasound and test – retest minimum detectable difference of the hamstring muscles

[STEPS]
TITLE: MecA detection Protocol
AUTHORS: Kabir Umar, Idris Abdullahi Nasir, Abdurrahman E Ahmad, Abdullahi Hassan Kawo, Abduqadir Magaji Magashi, Abubakar Umar Anka

[DESCRIPTION]
Polymerase chain reaction (PCR) was conducted for the detection of MecA gene from the Staphylococcus aureus Isolated from both healthcare workers and burns and wound patients using the primers listed in table 3.1. A total PCR reaction volume of 25µl containing primers 2 µl, Pre-mix 15 µl, sample 2 µl, and water 6 µl was used, and a cycling condition, with Initial denaturation at 94 ºC for 5 min, and 30 cycles of denaturation at 94 ºC for 30 sec, annealing at 55 ºC for 30 sec and elongation at 72 ºC for 1 min and final extension 72 ºC 10 min was adopted. PCR amplification was conducted in a thermal cycler (MyCycler Thermal Cycler, Bio-Rad, Portugal) after which agarose gel electrophoresis was run to detect the presence (Band size) or absence of MecA gene as described by Poulsen et al., 2003

MecA gene primers  
 
     Gene      Primers (3’-5’      Amplicon Size (BP)         mecA          F: GGGATCATAGCGTCATTATTC   R: AACGATTGTGACACGATAGCC      527   

 
 

[STEPS]
TITLE: An easy chromatographic method for purification of Immunoglobulin Y (IgY) using HiTrap™ Columns.
AUTHORS: Angel  Justiz-Vaillant

[STEPS]
?. Fill the syringe or pump tubing with de-ionized water. Remove the stopper and connect HiTrap™ column to syringe (use the connector supplied).
?. Snap off tab on the column outlet.
?. Wash out the ethanol with 26 ml of de-ionized water.
?. Equilibrate column with 26 ml of binding buffer. The recommended ﬂow rate is  5ml/min.
?. Apply the IgY sample using a syringe ﬁtted to Luer connector or by pumping it onto the column.
?. For better results, use a ﬂow rate of 0.5 to 5.1 ml/min during sample application.
?. Wash with at least 51 ml of binding buffer or no material remains in the efﬂuent.
?. Maintain a ﬂow rate of 5 to 11 ml/min for washing.
?. Elute with 51 ml of elution buffer using a one-step or using a linear gradient though larger volumes are often required to break the interaction.
?. After elution, regenerate the column by washing with 36 ml of wash buffer.
?. Re-equilibrate the column with 26 ml of binding buffer.
?. The column is now prepared for a new puriﬁcation.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes an optimized protein extraction method for (meta-) proteomic analyses. It is based on several existing protocols (see references below) that were combined and adapted and is also compatible with low biomass samples.</p>
<p> </p>
<p><strong>References: </strong></p>
<p>Erde et al. 2014, J. Proteome Res. 13, 1885-1895</p>
<p>Kleiner et al. 2017, Nat. Comm. 8, Article Number 1558</p>
<p>Kulak et al. 2014, Nat. Methods 11, 319-324</p>
<p>León et al. 2013, Mol. Cell. Proteomics 12, 2992-3005</p>
<p>Masuda 2008, J. Proteome Res. 7, 731-740</p>
<p>Wang et al. 2015, Int. J. Anal. Chem. 2015, Article ID 763969</p>
<p>Wisniewski et al. 2009, Nat. Methods 6, 359-362</p>

[BEFORE_START]
<p>Prepare stock solutions</p>
<p>Prepare lysis buffer</p>
<p>Have ice bath ready</p>
<p>Pre-heat thermoshaker (95 °C)</p>

[GUIDELINES]
<p>This protocol can be used to extract proteins from biological samples for (meta)proteomics. It is an adaptation of existing protocols*. It can also be used for (very) low-input samples.</p>
<p> </p>
<p><strong>*References:</strong></p>
<p>Erde et al. 2014, J. Proteome Res. 13, 1885-1895</p>
<p>Kleiner et al. 2017, Nat. Comm. 8, Article Number 1558</p>
<p>Kulak et al. 2014, Nat. Methods 11, 319-324</p>
<p>León et al. 2013, Mol. Cell. Proteomics 12, 2992-3005</p>
<p>Masuda 2008, J. Proteome Res. 7, 731-740</p>
<p>Wang et al. 2015, Int. J. Anal. Chem. 2015, Article ID 763969</p>
<p>Wisniewski et al. 2009, Nat. Methods 6, 359-362</p>

[STEPS]
?. 
?. 
?.
TITLE: TSS transformation of non-competent E. coli cells
AUTHORS: Alice Pawlowski

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transformation & Storage Solution (2X TSS) enables researchers to take advantage of the simple system described by Chung et al., 1989 (DOI:</span><a href="https://doi.org/10.1073/pnas.86.7.2172" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;:UNDERLINE;">10.1073/pnas.86.7.2172</span></a><span style = ":;:UNDERLINE;">)</span><span>  for the transformation of  </span><span style = "font-style:italic;">E. coli </span><span>cells</span><span style = "font-style:italic;">.</span><span> Early log-phase cells are suspended in 1X TSS, a solution containing polyethylene glycol, dimethyl sulfoxide, and divalent cations in a bacterial growth medium.</span></div><div class = "text-block"><span>This protocol is an alternative to the transformation method with chemically CaCl</span><span style = "vertical-align:sub;">2</span><span>-competent cells.</span></div><div class = "text-block"><span style = "font-weight:bold;"> </span><span style = "font-weight:bold;">Advantage</span><span>: You can use any fresh </span><span style = "font-style:italic;">E. coli</span><span> cells</span></div><div class = "text-block"><span style = "font-weight:bold;"> </span><span style = "font-weight:bold;">Disadvantage</span><span>: Low efficiency. Use only for transformation of plasmids, not for ligation mixtures in molecular cloning. It is possible to transform at least two plasmids at the same time.</span></div><div class = "text-block"><span>CaCl</span><span style = "vertical-align:sub;">2</span><span>-Transformation does not work for </span><span style = "font-style:italic;">E. coli </span><span>strains W3110 and W3110 Z1, thus TSS transformation is a method of choice.</span></div></div>

[STEPS]
?. [Transformation]
Inoculate  3 ml LB-medium with colonies from a fresh agar plate.
?. [Transformation]
Incubate at 37 °C and 230 rpm for 1.5 to 2.0 h (exponential growth). Culture should become turbid.
?. [Transformation]
Meanwhile prepare 1.5 ml tubes with 200 µl of 2x TSS-buffer and keep on ice. Add 200 µl cells and 0.5 - 1.0 µl Plasmid. Vortex and incubate on ice for 20 - 30 min. Longer incubation time will reduce transformation efficiency!
?. [Transformation]
Incubate 45-60 min at 37 °C on the Thermomixer with shaking (900 rpm). Addition of LB is not required.
?. [Transformation]
Plate on agar plates containing the appropriate antibiotic
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocols describe the steps to perform a western blot in Chlamydomonas reinhardtii cell lysate and supernatant samples.</p>

[BEFORE_START]
<ul>
<li>Check antibody dilutions</li>
<li>Check buffers disponibility</li>
<li>Prepare 5% milk solution</li>
</ul>

[GUIDELINES]
<p>Prepare cell material by cultivating in liquid media. </p>

[STEPS]
?. 
?. 
?. 
?.
TITLE: S. elongatus stock revival
AUTHORS: Akashdutta  

[DESCRIPTION]
Stocks are more permanent methods of storing bacteria than plates. These stocks can be recovered by pouring them into small volumes of BG-11 and growing under low light levels. As the culture grows, it can be passaged into higher volumes and appropriate antibiotics can be added.


[STEPS]
1. Add your stock to 2 mL BG-11 medium in a test tube and grow it overnight.
 


2. Transfer this to a 50 mL  flask and make up the culture to 10 mL in volume.

3. Once it reaches a lime green colour (#32CD32), add a fresh medium to make the culture up to 50 mL culture in a 150 mL 

4. Further, make this culture up to 100 mL  in a 250 mL  flask once it returns to lime green.
TITLE: BG11 medium
AUTHORS: Roscoff Culture Collection

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium to grow freshwater cyanobacteria.</div></div>

[STEPS]
?. [Prepare using Sigma Aldrich stock]
Under hood, to 1L of sterile water, add 20 mL of Cyanobacteria BG-11 Freshwater Solution from SigmaFilter the medium on 0,2 microns
?. [Prepare from base chemicals]
{"blocks":[{"key":"3suc3","text":"Stanier RY, Deruelles J, Rippka R, Herdman M, Waterbury JB: Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria. Microbiology 1979, 111:1\u201361.","type":"unstyled","depth":0,"inlineStyleRanges":[{"offset":60,"length":87,"style":"bold"}],"entityRanges":[],"data":[]},{"key":"dsbhh","text":"Recipes for standard and alternative BG11 for culturing freshwater cyanobacteria, such as\u00a0Synechocystis sp. PCC 6803, as described.","type":"unstyled","depth":0,"inlineStyleRanges":[{"offset":90,"length":13,"style":"italic"}],"entityRanges":[],"data":[]},{"key":"7i89s","text":"Media is usually not suitable for marine cyanobacteria.","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]},{"key":"9jkvu","text":" ","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]}
TITLE: Viral Titration of SARS-COV-2 by Plaque Assay (Semi-Solid Agarose)
AUTHORS: Björn Meyer

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the process of plaque assay for the viral titration of SARS-CoV-2.</div></div>

[STEPS]
?. [Preparing Plaque Overlay (2x)]
Mix  with .
[MEM]
[FBS]
The final concentration will be 4% in the 2x overlay.
?. [Preparing Plaque Overlay (2x)]
Prewarm the media to .
37 °C
?. [Preparing Plaque Overlay (2x)]
Dissolve  in .
[Agarose]
[H2O]
The final concentration will be 2% in the 2x overlay
?. [Preparing Plaque Overlay (2x)]
Melt Agarose in the microwave until liquified.
?. [Preparing Plaque Overlay (2x)]
Quickly add  to the prewarmed media from Step 2.
[melted Agarose]
?. [Preparing Plaque Overlay (2x)]
Close the bottle containing the Agarose/media mixture and shake vigorously for , then again for 3-4 more time over the  time period.
?. [Preparing Plaque Overlay (2x)]
Let the solution cool at .
0 Room temperature
Solution can be stored at   and can be reused when needed.
?. [Day 2 - Viral Dilutions]
Set up a 96-well plate in order to dilute your viral solution (serial dilutions).
?. [Day 2 - Viral Dilutions]
In each well, put .
[MEM (serum-free)]
?. [Day 2 - Viral Dilutions]
Add  in the first row (A) and mix thoroughly.
[viral solution]
Steps 11 to 22 are to be performed in a BSL-3 laboratory/setting.
?. [Day 2 - Viral Dilutions]
Discard your tips.
?. [Day 2 - Viral Dilutions]
Transfer  to the second row (B).
[previous mix (solution in row A)]
?. [Day 2 - Viral Dilutions]
Repeat that step from row C until row H (SARS-CoV-2 often reaches titers to 106).
?. [Day 2 - Viral Infection]
Transfer .
[each dilution into each well]
?. [Day 2 - Viral Infection]
Incubate at  for . Every , rock the plate a bit.
37 °C
?. [Day 2 - Viral Infection]
While cells are incubating with virus, prewarm 2x overlay media.
?. [Day 2 - Viral Infection]
After 1 hour absorption time, add  on top of the 250uL of inoculum (final volume 500uL per well).
[2x overlay media]
?. [Day 2 - Viral Infection]
Incubate at  for ~.
37 °C
?. [Day 5]
Prepare a solution of crystal violet diluted in EtOH as follows:  +  + .
[crystal violey]
[EtOH]
[water]
?. [Day 5]
Put about  into each well on top of the overlay media.
[formalin 4%]
?. [Day 5]
Let the well-plate sit for  to  at .
0 Room temperature
?. [Day 5]
Remove media from the well plate.
?. [Day 5]
Add a solution of 0.25% Crystal Violet and 20% Ethanol in water to each well in order to stain viable cells.
?. [Day 5]
Let the well-plate sit for  at .
0 Room temperature
?. [Day 5]
Plunge the well-plate into a first bucket filled with 1% bleach diluted in water.
?. [Day 5]
In order to properly clean the plate, plunge the well-plate into a second bucket filled with water.
?. [Day 5]
Count plaques against a white background.
?. [Day 1]
Plate 24 well plates with 7.5x104 Vero E6 per well in 10% FBS/DMEM.
?. [Day 1]
Let cells grow  at .
37 °C