create account

Bioinformatics experiments. Introduction by alexbiojs

View this thread on steemit.com
· @alexbiojs · (edited)
$15.71
Bioinformatics experiments. Introduction
<center>![ERK_1_1.png](https://cdn.steemitimages.com/DQmYC6aSeMrLt3y8jzmYsKuz7LVzHmAsCH6iHcDwSv4SCYc/ERK_1_1.png)</center>
<center>(The image above was created by me with the help of [PyMol](https://github.com/schrodinger/pymol-open-source) (open-source tool for molecules visualization/exploration). You can use the image if you want)</center>

The purpose of this series of posts is to demonstrate the power/beauty of bioinformatics (I’m just an amateur, though). 
There’re 2 terms, most biologists are familiar with, namely **“In vivo”** and **“In vitro”**.
**"In vitro"** is used to describe the studies of living/dead organisms done outside of their normal context/environment (like in test-tubes).
**"In vivo"** is used to describe the studies of living organisms done in their normal context/environment.
And with the advent of computers one more term was introduced -> “In silico”.
**“In silico”** is used to describe experiments done with biological data with the help of computer power. 
[2, 3, 4]
**Bioinformatics** is an interdisciplinary field of study, taking advantage of mathematics, statistics, computer science, computational linguistics and some others [1]. 

And the purpose is to help scientists to understand biological data.

All you need to do “In silico” experiments is your desire, internet-connection and computer.

With biochemistry/molecular biology moving forward, a huge amount of data was collected. This was one of the impulses for bioinformatics development. Not only we have nowadays a huge amount of information about protein/DNA/RNA sequences, but we also have a huge amount of literature. And it’s impossible to read all that and to investigate all that biochemical information manually.

![DUSPs_alignment_Clustal.png](https://cdn.steemitimages.com/DQmekpZWy4zwKogmrcwJo9exDkh4VvJHGoa7zaxMYQWikKr/DUSPs_alignment_Clustal.png)
<center>(The image above was created by me with the help of [Clustal Omega](https://www.ebi.ac.uk/Tools/msa/clustalo/). You can use the image if you want)</center>


Even though we see “informatics” in “bioinformatics”, you don’t need to be a programmer to do bioinformatics (but that might be useful). For all those biological data stored on serves a huge amount of web-tools was developed. One of the central resource for bioinformatics knowledge is [National Center for Biotechnology Information](https://www.ncbi.nlm.nih.gov/) (NCBI).

It’s hard to describe the whole range of opportunities bioinformatics gives to its users. 

With bioinformatics there’s no need to waste a lot of resources to carry out lots of those experiments done in test-tubes, which saves us a lot of reagents and, most importantly, bioinformatics saves us a lot of time. 

You can “feel” the power of bioinformatics especially when it comes to [Cyc](https://lucid.ai/).
>…the world’s largest smartest common sense knowledge base.
Cyc helped the Cleveland Clinic sift through five million patient records to find the perfect 82 drug trial candidates for a new cardiovascular therapy.
A search like this usually takes 10 weeks.
It took Cyc 10 minutes.
[source – "Meet Cyc" video on YouTube]

For more information about Cyc watch "Meet Cyc" video on YouTube (or read about Lucid.AI).

In this series of posts we are going to explore some biochemical/bioinformatics concepts and some tools for bioinformaticians.
 I’m not going to provide explanations/definitions for such common-used terms like proteins, enzymes, but I will try to provide them for some bioinformatics-specific terms and, possibly, some analogies from non-biochemical/bioinformatics-related life.


### References:

1. https://en.wikipedia.org/wiki/Bioinformatics

2. https://en.wikipedia.org/wiki/In_vitro

3. https://en.wikipedia.org/wiki/In_vivo

4. https://en.wikipedia.org/wiki/In_silico
👍  , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and 523 others
properties (23)
post_id74,682,197
authoralexbiojs
permlinkbioinformatics-experiments-introduction
categoryscience
json_metadata{"tags":["science","bioinformatics","biology","biochemistry"],"image":["https:\/\/cdn.steemitimages.com\/DQmYC6aSeMrLt3y8jzmYsKuz7LVzHmAsCH6iHcDwSv4SCYc\/ERK_1_1.png","https:\/\/cdn.steemitimages.com\/DQmekpZWy4zwKogmrcwJo9exDkh4VvJHGoa7zaxMYQWikKr\/DUSPs_alignment_Clustal.png"],"links":["https:\/\/github.com\/schrodinger\/pymol-open-source","https:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\/","https:\/\/www.ncbi.nlm.nih.gov\/","https:\/\/lucid.ai\/","https:\/\/en.wikipedia.org\/wiki\/Bioinformatics","https:\/\/en.wikipedia.org\/wiki\/In_vitro","https:\/\/en.wikipedia.org\/wiki\/In_vivo","https:\/\/en.wikipedia.org\/wiki\/In_silico"],"app":"steemit\/0.1","format":"markdown"}
created2019-05-13 18:08:45
last_update2019-05-14 09:11:42
depth0
children4
net_rshares30,429,683,382,767
last_payout2019-05-20 18:08:45
cashout_time1969-12-31 23:59:59
total_payout_value11.840 SBD
curator_payout_value3.869 SBD
pending_payout_value0.000 SBD
promoted0.000 SBD
body_length3,800
author_reputation7,470,218,989,273
root_title"Bioinformatics experiments. Introduction"
beneficiaries[]
max_accepted_payout1,000,000.000 SBD
percent_steem_dollars10,000
author_curate_reward""
vote details (587)
@chappertron · (edited)
This is what we need here!

Please give us more of it!

Thanks & respect

Chapper

Edit: Oh, would you please be so kind to add some references?
👍  
properties (23)
post_id74,685,296
authorchappertron
permlinkre-alexbiojs-bioinformatics-experiments-introduction-20190513t192545651z
categoryscience
json_metadata{"tags":["science"],"app":"steemit\/0.1"}
created2019-05-13 19:25:45
last_update2019-05-14 04:25:00
depth1
children1
net_rshares7,614,782,884
last_payout2019-05-20 19:25:45
cashout_time1969-12-31 23:59:59
total_payout_value0.000 SBD
curator_payout_value0.000 SBD
pending_payout_value0.000 SBD
promoted0.000 SBD
body_length144
author_reputation22,330,008,525,791
root_title"Bioinformatics experiments. Introduction"
beneficiaries[]
max_accepted_payout1,000,000.000 SBD
percent_steem_dollars10,000
author_curate_reward""
vote details (1)
@alexbiojs · (edited)
Hi.
thanks for support.
no problem.
I added them.
👍  
properties (23)
post_id74,713,466
authoralexbiojs
permlinkre-chappertron-re-alexbiojs-bioinformatics-experiments-introduction-20190514t084522416z
categoryscience
json_metadata{"tags":["science"],"app":"steemit\/0.1"}
created2019-05-14 08:45:24
last_update2019-05-14 09:12:09
depth2
children0
net_rshares21,324,580,269
last_payout2019-05-21 08:45:24
cashout_time1969-12-31 23:59:59
total_payout_value0.000 SBD
curator_payout_value0.000 SBD
pending_payout_value0.000 SBD
promoted0.000 SBD
body_length49
author_reputation7,470,218,989,273
root_title"Bioinformatics experiments. Introduction"
beneficiaries[]
max_accepted_payout1,000,000.000 SBD
percent_steem_dollars10,000
author_curate_reward""
vote details (1)
@steemstem ·
re-alexbiojs-bioinformatics-experiments-introduction-20190514t113815040z
<div class='text-justify'> <div class='pull-left'> <center> <br /> <img width='200' src='https://res.cloudinary.com/drrz8xekm/image/upload/v1553698283/weenlqbrqvvczjy6dayw.jpg'> </center>  <br/> <br /> </div>

This post has been voted on by the **SteemSTEM** curation team and voting trail. It is elligible for support from <b><a href='https://www.steemstem.io/#!/@curie'>@curie</a></b> and <b><a href='https://www.steemstem.io/#!/@utopian-io'>@utopian-io</a></b>.<br /> 

If you appreciate the work we are doing, then consider supporting our witness [**stem.witness**](https://steemconnect.com/sign/account_witness_vote?approve=1&witness=stem.witness). Additional witness support to the [**curie witness**](https://steemconnect.com/sign/account_witness_vote?approve=1&witness=curie) and [**utopian-io witness**](https://steemconnect.com/sign/account_witness_vote?approve=1&witness=utopian-io) would be appreciated as well.<br /> 

For additional information please join us on the [**SteemSTEM discord**]( https://discord.gg/BPARaqn) and to get to know the rest of the community!<br />

Please consider setting <b><a href='https://www.steemstem.io/#!/@steemstem'>@steemstem</a></b> as a beneficiary to your post to get a stronger support.<br />

Please consider using the <b><a href='https://www.steemstem.io'>steemstem.io</a></b> app to get a stronger support.</div>
properties (22)
post_id74,720,143
authorsteemstem
permlinkre-alexbiojs-bioinformatics-experiments-introduction-20190514t113815040z
categoryscience
json_metadata{"app":"bloguable-bot"}
created2019-05-14 11:38:18
last_update2019-05-14 11:38:18
depth1
children0
net_rshares0
last_payout2019-05-21 11:38:18
cashout_time1969-12-31 23:59:59
total_payout_value0.000 SBD
curator_payout_value0.000 SBD
pending_payout_value0.000 SBD
promoted0.000 SBD
body_length1,367
author_reputation179,657,124,557,517
root_title"Bioinformatics experiments. Introduction"
beneficiaries[]
max_accepted_payout1,000,000.000 SBD
percent_steem_dollars10,000
@utopian-io ·
#### Hi @alexbiojs!

Your post was upvoted by Utopian.io in cooperation with @steemstem - supporting knowledge, innovation and technological advancement on the Steem Blockchain.

#### Contribute to Open Source with utopian.io
Learn how to contribute on <a href='https://join.utopian.io'>our website</a> and join the new open source economy.

**Want to chat? Join the Utopian Community on Discord https://discord.gg/h52nFrV**
properties (22)
post_id74,746,511
authorutopian-io
permlinkre-bioinformatics-experiments-introduction-20190514t230145z
categoryscience
json_metadata{"app":"beem\/0.20.17"}
created2019-05-14 23:01:45
last_update2019-05-14 23:01:45
depth1
children0
net_rshares0
last_payout2019-05-21 23:01:45
cashout_time1969-12-31 23:59:59
total_payout_value0.000 SBD
curator_payout_value0.000 SBD
pending_payout_value0.000 SBD
promoted0.000 SBD
body_length424
author_reputation151,356,124,843,620
root_title"Bioinformatics experiments. Introduction"
beneficiaries[]
max_accepted_payout1,000,000.000 SBD
percent_steem_dollars10,000