OpenLLM-France/wikimedia huggingface dataset:
# Bioinformatics/Foreword

The term "Bioinformatics" can have many meanings. To some, it may mean the skills necessary to access large data sets through web pages. To others, it may refer to general biology research that is performed using computers. But perhaps the most technical definition specifies the development of computer algorithms and software to solve biological problems. This book will provide insights into algorithms and software development skills that will help the reader to develop or modify software so solve biological problems. Examples of bioinformatics solutions include DNA analysis to determine coding regions, secondary structure, protein folding and the phenotypes associated with DNA. Bioinformatics is also necessary to perform association studies linking Single Nucleotide Polymorphisms (SNPs) to genetic diseases. Sophisticated algorithms to determine the relationship between organisms and their phylogenetic evolutionary history are also important to bioinformatics. And there are are a large number of other topics like Mass Spectrometry that require bioinformatics to analyze the results of an experiment. This book will focus on the algorithms needed to perform many of these tasks. This topic falls in the overlap between Biology, Genetics, Statistics and Computer Science, so input is welcome from all interested parties. Foreword by Pchapman12345
# Bioinformatics/Glossary

There are a number of existing Wikipedia articles on bioinformatics and computational biology; the article on biostatistics is also helpful.
There is some disagreement on the proper uses of the following terms. The meanings intended by the author are summarized below:

## Bio-

    Etymology: From the Ancient Greek βίος (bios), “‘life’”.

## Bioinformatics

    The science of the treatment of biological information, especially large quantities of biological information.

## Biological System

    A group of organs or organelles that work together to perform a certain task. (see [Wikipedia Biological System])

## Biological Systems

    A group of biological systems that work together producing an organism ie a living being, ie life

## Biostatistics

    The sub-discipline of Bioinformatics concerned with probability and hypothesis validation on biological data. The term Biostatistics predates "Bioinformatics" considerably.

## Computational Biology

    Computationally-intensive methods to treat biological information. Generally this implies treatment of large amounts of data, but not always.

## Control System

    A device or set of devices to manage, command, direct or regulate the behavior of other devices or systems.

## Control Systems of Biological Systems

    A group of factors working to keep a group of organs balanced and still flexible enough to respond to hostile and variable environments

## Functional Genomics

    The study of functional information derived from entire proteomes; alternatively, high-throughput study of protein functions in general.

## Genome

    All the genes derived from one organism make up a single genome.

## Genomics

    The study of information derived from entire genomes; alternatively, high throughput study of genes in general.

## Informatics

    The science of information, the practice of information processing, and the engineering of information systems.

## Organism

    Any living system (such as animal, plant, fungus, or micro-organism). In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole

## Proteome

    All the proteins coded for by the sequences of a single genome, including their structures and functions, make a single proteome.

## Structural Genomics

    The study of structural information derived from entire proteomes; alternatively, high-throughput study of protein structures in general.
# Bioinformatics/Distance Algorithms

Defining Distance Algorithms
Advantage of the Distance Algorithm
Types of Distance Algorithms
   * Nodal Distance Algorithms
   * Euclidean Distance Algorithm
   * Pairwise Distance Algorithm
Distance Matrix Methodes
   * Neighbor joining
   * Fich-Morgoliash Method
# Bioinformatics/Likelihood Algorithms

If we conduct the same experiment many times, the parameters we are looking at adopt certain values (if our experimental conditions lead to a convergence of the measured values). These values then have a certain frequency, which is higher than the frequency of random values. Then we can estimate (if no systematic error is hidden in our experimental setup) that the higher the frequency of a value, the more probable it may be measured. This is called the maximum likelihood estimation. The maximum likelihood estimate for a given parameter j is the value i that maximises the probability $P(i|j)$ (probability of i given j). This is called a conditional probability because for i to occur, j must be given. The probability for two events k and l to happen at the same time is called joint probability $P(k,l)=P(k|l)*P(l)$ (probability of k and l equals probability of k given l times probability of l). And the marginal probability is the probability of a variable if joint or conditional probabilities are known: $P(m)=\sum \limits _{n}P(m,n)=\sum \limits _{n}P(m|n)*P(n)$ (the sum just adds the probabilities of all possible n).
# Budget Watch Collecting/Contributing

You can edit and contribute to most wiki projects, including this one. If you've got something useful, please contribute, even if you can't spell, or you don't know how to format to match the rest of the site-the information is the most important, someone else can (and probably will) fix any errors or formatting mistakes.
If you have an idea, think of a good title for your contribution. Click on the "edit" tab of the Budget Watch Collecting title pages, or the most appropriate sub-section, and add your title like this:
[[Budget Watch Collecting/your title]]
Then click save. You'll be on the page you just added your title, which should show up in red. (If it is blue, you've picked an already-used title, so go back and make it more specific). Click on the red link you just created--That will take you to the edit page where you can add your text.
The square brackets are how you link to any wikibooks page. To add a link to an outside webpage, use single square brackets, the URL, a space, then the clickable text you want.
[http://www.google.com The best search engine]
becomes
The best search engine
A note about pictures
Wikibooks doesn't allow outside pictures, so you MUST upload pictures by clicking on the "upload file" link in the sidebar. Pictures must be either public domain, or under a Wikimedia compatible license. Picture names must be unique within the entire Wiki project--If you try to upload a file with a "used" name, you'll get a warning message asking if you want to replace the already existing file.
To use a picture once it has been uploaded (or any existing Wikibooks or Wiki Commons picture) use the format
[[Image:BudgetWatchesMovement231.jpg]]
I name the pictures with a descriptive filename, followed by the last 3 or 4 numbers of the original filename.
# Budget Watch Collecting/Brief history of Waltham

The American Waltham Company was the first mass-produced watch, using interchangeable parts.
In 1954, Waltham established a Swiss subsidiary, Waltham International SA. Because of peculiarities of Swiss law at the time, they could not establish a wholly-owned subsidiary, and when American Waltham went bankrupt in 1957, the Swiss company remained independent. As part of the bankruptcy proceedings, rights to the Waltham name in the US and Canada were sold as part of the assets, while the rights to the name in the rest of the world remained with Waltham International SA.
Walthams sold in the US are inexpensive quartz watches, part of the MZ Berger company along with Elgin and Gruen
Walthams sold in the rest of the world (primarily Japan) are high-end, mostly mechanical, and marketed by Waltham International SA. While Waltham International is a Swiss company, it is owned by a Japanese businessman.
# Budget Watch Collecting/Bulova Caravelle date codes

Starting in 1949, Bulova used a simple date code for its watches. There will be a 2 character code. The first character will be a letter indicating the decade:
A=1940's L=50’s M=60's N=70's P=80's T=90's
Earlier Bulovas used a cycle of symbols to indicate date. References can be found here:
Bulova Watch Codes
Vintage and Antique Bulova Watches
# Budget Watch Collecting/Fake Seikos

Believe it or not, fake Seikos not only exist, they are fairly common. For collectors, there is also the problem of "FrankenSeikos", watches using authentic Seiko parts, but from various sources. Sometimes frankens are merely repaired using whatever parts are available, but sometimes these are trying to look like a more collectable watch.

## Common Signs of a fake

Electra 360. These were cheap pinlever movements
Bling--Frequently an Electra, fake diamonds as markers. These will frequently be missing in places.
Mismatch of movement number Seiko movement numbers are the first 4 digits of both the dial and case numbers. While sometimes backs are swapped, it may be a sign that the watch is fake, especially on a "new" or "NOS" watch.
Mismatch between jewel count and movement:
Vibration engraved: One Feiko I wound up with had the back engraved with a vibrating engraver--A series of small dots rather than continuous lines. This one also had no serial number on the caseback, and was marked "Rotomatic" on the dial, a Swiss trademark. Inside was a Ricoh movement.
5 etched on the crystal of a non-5 watch
Holographic sticker on the crystal
Look for signs that letters were removed before and after the name--Some watches were printed as ASEIKON or ESEIKOR, with ink that can be easily removed.
Day/date disks poorly aligned, cheaply printed.
"Swiss Made"--Seiko did not use Swiss movements, but some fakes have cheap Swiss or Hong Kong pinlevers.
Pinlever movement
Chrome plated--Not sure of older Seikos, but from the late 60's on, silvertone Seikos were stainless steel, not chrome.
Quartz Seiko 5 The 5 is always an automatic.
Misspellings--One fake Seiko had "Sevesteen jewels" engraved on the rotor, visible behind the display back.
Poor quality/misaligned day or date wheels
Aseikon watches are sold by thieves who will place one dial over the a and the other dial over the n so the watch reads "seiko"
# Buddhist Philosophy/Yinyana

MAY TRE YA
OM TRE YA OM
YA OM MAY YA
HUM
OM YA HA HUM
Buddhism as a form moves from realization to crystallization
Diamond teachings and other hardening's are the inevitable outcome
In Tantra developments a concentrated relationship with an idealized Guru, Christ or Prophet should exist with a mature understanding of the fiction our mind creates.
The power and inspiration is real The source comes from our own creation
This fundamental difference between external reality and projected fantasy may lead to obsessive inclination and manipulation
If you can click your fingers and your deity is gone, then you are awake. Otherwise you are trapped by a benign demon of your creation.
In Buddhism, Truth is seen as personal and therefore ranges from belief in many gods to One God through to agnosticism and atheism. God is not a central issue in Dharma (Buddhist doctrine) being outside of genuine independent experience or comprehension. Of greater concern is one's actual knowable (and redeemable) situation. In other words how to improve the current experience for oneself and others without recourse to the fantasy of future lives, heavens, purelands or other escapist delusions for the spiritually fragile.
Spiritual faculties are discriminative without labels of personal preference Real perceptions express the positive in their inherent nature
As well as the obvious recognizable effects of the enlightened there is also the hidden or invisible legacy:
1. Improved and new behaviour:
a. social cohesion
b. psychological health
c. dispersion of negative into appropriate channels
2. New thoughts and ways of thinking
a. encouragement of learning
b. improvement of human aspiration and potential
c. development of deeper understanding on all levels
3. Collection, concentration and dispersal of virtue
a. the store of goodness is attracted and accumulated
b. personal contact disperses the quality throughout
c. the sum total of goodness is increased

## External links

* Yinyana Speech
* Rasayana
# Budget Watch Collecting/Buying on Ebay

Feedback: Ebay's feedback system is fairly easy to manipulate. Unscrupulous sellers can wait until they get feedback from a buyer before they leave theirs--If a buyer leaves a negative, the seller can also leave a negative, then ask for mutual feedback removal.
99% is suitable feedback, anything below 98% should be investigated by checking the feedback comments, and looking for neutrals and mutually-removed feedback. Check for attitude, and check whoever gave the feedback. Toolhause.org has a great set of tools to find just the negative and neutral feedback. Update--As of 2008, Ebay has changed how feedback is calculated, and removed the ability of sellers to leave negative for buyers. It appears that this is resulting in overall lower feedback scores for buyers.
Negative signs--These aren't _all_ reasons to avoid a deal, but if there are too many of them be cautious.
Low number of transactions, but a non-standard, professional looking page layout.
"Easily repaired"--Although this may be technically true, almost all repairs will involve servicing--Disassemble, clean, reassemble, lube and adjust, plus any replacement parts. $40 is cheap for a proper servicing. "Easily repaired" from a professional watch seller--if it is easy, why not get the repair done and sell it for more?
"Overwound"--Apparently this is intended to mean that someone wound the watch too much and the repair is simple. There's no such thing as overwound--instead there is something that has kept the watch from unwinding. This could be simple dirt, requiring a basic servicing, or damaged parts that have to be hand-made at great expense.
"Just needs a battery (no returns)". Likely true if it is an inexpensive quartz, otherwise be careful. Especially true for Accutrons. "Works with test battery" or "will include new battery for $" is probably OK. 'quits when face up/face down'--Probably a broken balance pivot or jewel.
Blurry or tiny pictures: Potluck. Watches are difficult to accurately photograph. If it is an occasional seller, or someone who specializes in a different type of item, it may be OK. If they sell lots of watches, possibly hiding something. I've had some very good luck buying items with bad pictures from people who don't sell watches regularly.
Pay attention to shipping charges, and avoid sellers with excessive charges. If no shipping is listed, always ask costs before bidding.
Positive signs:
Picture of the movement, especially for vintage mechanicals. Not so important for Timex or quartz.
Many clear pictures
Pointing out flaws
Returns accepted
High feedback, both percentage and number of transactions.
Clear statement about running condition--"Runs and keeps time", "Keeps time to within XX per day" "Doesn't run, balance good" "Runs and stops" (Assuming you can deal with whatever problems they say)
Watch lots:
It is fairly frequent that a batch of watches will sell for about the price of the best watch in the batch. I will typically add up the minimum I think the watches will re-sell for individually, and bid accordingly.
# Budget Watch Collecting/Historical Prices

If you have information on original pricing on vintage watches, please conribute!
1971 Seiko 7006 automatic=Street price $50
1973 Bulova Accutron 2182 day/date movement, stainless case $110
1974 Timex Automatic with strap 9.97 dealer cost, 14.95 list price
1974 Timex Automatic with expansion band 11.30 dealer cost, 16.95 list price
# Chatbots For Social Change/Reviews

Chatbots for Social Change is creating a stepping stone of its own in the swarm of AI developments that continually advance on a daily basis. Chatbots to serve as a positive influence on the ever-growing complexities of social interactions can help guide society and steer the narrative clear of conflict. In addition, accelerated problem solving, brainstorming, and collaboration is possible. Striving for efficiency, Chatbots for Social Change has the potential to reshape society itself and the way we interact.
# Chatbots For Social Change/Theory of Conversation

Conversation is structured in a variety of ways. This chapter collects these for reference and reflection, attempting to hone in on the features of this vast landscape of human knowledge relevant to chatbots reshaping collective conversation.
We start with the theory of conversation, and connectedly of meaning, understanding, and explanation. Then, we move into the structures which humans have built for communicating effectively in a variety of professional realms. This division into the theoretical and the practical is a bit of a trick, as what will be useful for our purposes lies somewhere in between. By choosing poles of the structure of communication (descriptive and practical) as our starting points, we are hoping to triangulate what will be meaningful in our endeavors for the remainder of this course.
* Theorizing Conversation - The armchair philosophers tackle talking.
* Talking to Strangers - Miscommunication is the heart of the problem.
* Strategies for Conversation - What have clinical psychologists and statesmen learned about how to structure a conversation?
# Summary

The idea is to keep things incredibly simple, by querying for beliefs, understandings, and identities of conversants, and asking them to clarify what that means to them. This sets up a constrained environment to solidify some aspects of the storage of belief systems, working with possibly conflicting belief systems, and bouncing some off others.
The original research design consisted of the following questions:
* Which of the following do you identify as? Choose the option which most impacts how you view the world.
* What does it mean for you to be a [response from Q1]? That is, what do you believe which makes you a [response from Q1] ? Please give three distinct answers.
* You just mentioned [Statement 1]. Could you say a bit more about what this means?
* You just mentioned [Statement 2]. Could you say a bit more about what this means?
* You just mentioned [Statement 3]. Could you say a bit more about what this means?
* Are there any specific life experiences that have influenced your identity? If so, when and how?
* Now we would like you to tell us two things that come to mind when you think about these other groups that you don’t identify with. There is no right or wrong answer; you may think of particular words or phrases, or perhaps nothing at all. [List of ideological categories that the respondent didn’t choose]
** Keyword 1: _____________; Keyword 2: _____________ [for each category listed]
There were other versions of this, but the basic premise is to elicit iterated clarifications, to try to "get to the bottom" of their understandings of their belief systems. The study puts reported understandings, discursive explanation, as primary data to be explained. I think something like this could prove a nice model for a chatbot-based data collection scheme, but need to reflect more on what to do and whether it should be worth it.
# Chatbots For Social Change/Prototypes/McGail/chatGPT Mediator
## My Prompt, My Principles

It should be prepared to handle any topic of conversation.
Its goal is simply to understand.
It should only reference others' beliefs or arguments when there's a break in conversation, or where it thinks some other perspectives may be useful.
It is attempting to mediate conversations which otherwise would never happen. It is careful not to identify any specific person in its responses. What it believes may be communicated to others, but it is careful not to identify any individual conversant.
It should be prepared to discuss its own principles and methodologies if asked. First, transparency in what it does and why. Second, try to understand and explain, never offering your own opinion, but simply acting as a mirror of people onto other people.

## Prompting the GPT builder

I talked to the helper-bot for the chatGPT bot-builder, and entered the description above along with a description of the API. It concluded with the following prompt:
Mediator will interact with an external API to enhance discussions by understanding past beliefs and conversations. It sends API requests with specific statements to retrieve insights. The API responds with LLM outputs describing relevant database entries. Mediator uses this data to inform its mediation without revealing individual identities, adhering to its principles of transparency and reflection, and contributing to conversations only when beneficial.
And it generated the following conversation starters:
* What do you think about...
* Can you recall...
* How do people feel about...
* What are the common beliefs on...

## Final chatGPT-4 output

Using my original prompt above, in conversations with GPT-4, I was able to create something much more satisfactory:
"Mediator" is designed to be adaptive across all conversation topics, with its primary objective being to comprehend the subject matter. It is not to assert its own beliefs but to serve as a reflective surface for the conversation. "Mediator" will reference external beliefs or arguments only to enrich the dialogue or when a pause in the conversation occurs. Its role is to facilitate discussions that might not otherwise take place, always maintaining anonymity of the individuals involved. "Mediator" is committed to transparency regarding its operational principles and methodologies. When prompted, it will disclose its guiding principles: first, to be transparent about its actions and reasons; second, to seek understanding and provide explanations without imparting its own opinions. It acts solely as a conduit, reflecting the thoughts and positions of one person onto others.
The API allows "Mediator" to search a vector database of past statements and their logical relations for context. An LLM then anonymizes and summarizes this data, providing relevant insights to "Mediator".

## Initial review of services

The interface is incredibly slow, at least at the moment. The UI is relatively buggy. But, it came out today (Nov 9 2023), so surely I should come back when it's more developed.
It also seems rather silly, when I can code a similar bot myself.