OpenLLM-France/wikimedia huggingface dataset:
# OpenClinica User Manual/SettingUpATestEnvironment
## Setting up a test-environment

Every once in a while you need to test something for OpenClinica and you don't want to clutter your production database, so you decide you need a test-environment. Here is how to do that, plus instructions how to clean up after your testing.
It takes four steps to create your test-environment:
* create a new database
* make a copy of the web-app
* make a data directory
* edit datainfo.properties

### Create a new database

In this example we'll name the test environment octest. Login to your server and go to the dir with psql and start it:
Check if the database was created correctly with "\list" (or just "\l" will do) and quit psql with "\q"

### Make a copy of the web-app

Change to the tomcat webapps directory and copy the OpenClinica structure:

### Make a data directory

Change to directory /usr/local/tomcat and create a data directory and give tomcat all rights:

### Edit datainfo.properties

The last thing to do is edit the file datainfo.properties. Go to the right directory and start your favourite editor:
Change: filePath=/usr/local/tomcat/openclinica.data/ into: filePath=/usr/local/tomcat/octest.data/
url=jdbc:postgresql://localhost:5432/openclinica into: url=jdbc:postgresql://localhost:5432/octest
sysURL=http://localhost:8080/OpenClinica/MainMenu into: sysURL.base=http://localhost:8080/octest/MainMenu
You are now ready to deploy your octest-app and you do this by stopping and starting tomcat.

### Cleaning up

After testing you should clean up the database and the app and you do this by:
stopping tomcat:
removing the app-directory:
removing the data-directory:
starting psql and removing the database:
starting tomcat:
# OpenClinica User Manual/RenamingDatasets
## Renaming datasets
### Cluttered lists

After you've been conducting your study for some time, you might find your list with datasets cluttered. Especially with names like "temp" or "temp2", etc. You can not rename these datasets and when you "delete" them, only the status changes. You may want to delete these sets or rename them.
In general it is a better approach to rename your datasets, because of regulations and because of complexity.

### Renaming

You could add a "z_" as prefix, so all your existing datasets go to the end of your list and new ones will be on top. If you look at the tables involved you'll see archived_dataset_file, dataset_crf_version_map, dataset_filter_map, dataset_item_status, dataset_study_group_class_map.
To see a list of all tables: login to your server; sudo as user postgres; start psql; connect to openclinica, describe all tables.
cd /usr/bin
sudo -u postgres ./psql
(in psql)
\c openclinica
\dt
The one you're aiming at is dataset, of course. To see the structure of the table, type "\d dataset" List your datasets with "select dataset_id, study_id, name from dataset;"
Find in this output the study_id of the study for which you want to rename your datasets, for example study_id=7. Your update statement will be "update dataset set name='z_'||name where study_id=7;"

### Deleting

If you really want to delete the datasets, you would have to issue a series of sql-statements like: "delete from archived_dataset_file where dataset_id in (select dataset_id from dataset where study_id=7);" And you would have to do this for all related tables and finally delete the records from table dataset.
And whatever you choose: before you do anything, make a backup.
# OpenClinica User Manual/ResetRootPassword
## Resetting root's password

When you do not have the password of root anymore and you still want to access OpenClinca you can reset it to 12345678.
You do this by connecting to the study database (e.g. the database openclinica rather than postgres), either by using the psql-commandline-utility or by pgAdmin. You can issue the next command either as user postgres or as user clinica.
For OpenClinica 3.1 and later:
For OpenClinica 3.0 and possibly earlier:
This command not only resets the password (to 12345678, passwd is set to the SHA1 hashed value of 12345678: '7c222fb2927d828af22f592134e8932480637c0d'), but also resets the counter of failed logins to 0 and unlocks the account).
# OpenClinica User Manual/Standards

In general, standard names make it easy to reuse code (CRFs and rules) from project to project, and if you know the conventions, they make the projects easier to understand.

## Standard variable names

Frequently used CRFs (Concomitant Medications, Adverse Events, Medical History etc.) in particular should use short, standard variable names (CDISC is a good source for example names).
CDISC has a set of standard variable names and fragments that should be used where possible. See CDASH (http://www.cdisc.org/cdash) and SDTM (http://www.cdisc.org/sdtm), also see section 10.3.1 ‘Standardised and Reserved codes’ in the SDTM3.1.1ImplementationGuide.pdf (http://www.cdisc.org/content1605). All variable names should be prefixed with fragments that indicate the domain that the variable is from (e.g. VS is Vital Signs).
* Standard Code Lists - define and reuse standard codelists (RESPONSE_TYPE, RESPONSE_LABEL,RESPONSE_VALUES_OR_CALCULATIONS groups) to simplify the work of those extracting data.
* Standard Rule xmls - define standard rules for frequently used CRFs (e.g. use short codes for trials to avoid conflicts with other co-hosted trials, see Avoiding problems with OIDs).
If a repeating set of questions is developed as a separate CRF, the developer can just create and test that section as a CRF once. This is made easier if the developer has input into the development of the original CRF, and can try to standardise the look of repeating sections, which can be later developed as one OpenClinica CRF.

### Defining Item_names to avoid problems when exporting to SAS and other formats (field lengths)

If a CRF's data will be exported for SAS, then the Item_names should be no more than 32 characters long to avoid import errors. For SAS programmers that will receive our data, shorter is better - because when writing code in SAS, there's no autocomplete.
When exporting to formats other than XML, avoid underscores in field and CRF names, as OpenClinica’s export inserts underscores to delimit CRFs and groups, and extra underscores make it difficult to automatically identify these delimiters and identify CRF, group and field names.
# OpenClinica User Manual/RuleLinks
### Links

This page contains links to external resources that provide informations about using rules in OpenClinica.
* About OC3.1, Amethyst and the new rules: https://www.openclinica.org/dokuwiki/doku.php?id=developerwiki:roadmap&s=rules#business_requirements_addressed1
* Same info as in the PDFs listed below, but in wiki-form, with an example of e-mail-action:
https://www.openclinica.org/OpenClinica/3.0/doc/5_5_rules_Help.html
* Directions about how to setup rules, plus link to a sample xml-file: https://openclinica.org/dokuwiki/doku.php?id=ocfeatures:rulefeedback&s=rules
* PDF explaining rules and operators and dates (very informative): http://www.openclinica.org/pipermail/users/attachments/20100810/421626be/XML_rules_documentation_v2-0001.pdf
* PDF explaining rules and operators and dates (also very informative, but slightly older than the previous one): https://openclinica.org/dokuwiki/lib/exe/fetch.php?id=developerwiki%3Aroadmap&cache=cache&media=developerwiki:rules_documentation.pdf
# Showing an image file
## Introduction

OpenClinica allows us to upload a file to the system. This file is only accessible through a link, it is not shown on the page. In this how-to we will see how we can show image files automatically.

## Where to store the uploaded files

In datainfo.properties there is an attribute called 'attached_file_location'. This specifies where the uploaded files will be stored on the server. If we leave this item blank the default location will be used: /usr/local/tomcat/<study_name>.data/.

### Challenge with default upload location

The default upload location is not in the root of the OpenClinica web application. Tomcat can therefore not access it, when we use a <img> tag. There are two ways around this.
* Change the default location
* Use a reverse proxy to serve images

#### Change the default location

When we want to store files in a place that is visible to Tomcat we change the line in datainfo.properties to:
Don't forget to change the <study_name> placeholder into something meaningful for your system.

#### Use a reverse proxy to serve images

Use OpenClinica_User_Manual/UsingAReverseProxy to install Nginx as a reverse proxy.
Add this line to the https server configuration of Nginx
Now images will be served directly by Nginx. If you use a lot of images, this is the preferred configuration.

## Code to add to the Excel CRF definition

Read OpenClinica_User_Manual/StylingWithJQuery for a better understanding of the code below. Put the code in LEFT_ITEM_TEXT.
The picture will be inserted before the standard buttons for replacing or removing a file. The picture is not immediately visible. It will be shown after you save the page and reopen it again.
# OpenClinica User Manual/StylingACRF
## How to style a CRF

The default visual representation of a CRF in OpenClinica is fairly simple and sometimes it cannot fulfil the users' requirements to the layout. Most commonly, it concerns the following requirements:
* Colours, both text and background
* Text size
* Links
* More than 3 or 4 columns †
* Column headers †
* Increased spacing between LEFT_ITEM_TEXT and input field
All these can be resolved, some of them easy, others more complex. The requirements marked with a † are not straight forward and may require a some CSS know-how to fit correctly.

### How to do this

Basically, all the requirements above are fulfilled by the use of in-line Cascading Style Sheets (CSS) in conjunction with basic HTML tags. The tags are typed directly into the cells of the XLS file. The following columns for input fields accept this kind of modification:
* LEFT_ITEM_TEXT
* RIGHT_ITEM_TEXT
* HEADER
* SUBHEADER
Below is an example of what is achievable. It addresses all the requirements mentioned before (and some more).
To see how this is done, please download the XLS file and carefully study the cell data: Click here to download from IFile.It

### Tips and Hints

* Personally, I use Firefox and the Firebug tool when styling CRFs. This enables me to change the styling within the browser and preview the outcome immediately. This is excellent for small tweaks to your styled colours, fonts and indents.
* You can't always rely on the preview of the CRF (before submitting). The layout of this isn't usually exactly the same as viewing the CRF in Data Entry View. This is especially true when doing text-indents of first input field in a row.
* You need to test the result in multiple browsers (at least Firefox and IE (with and without Compatibility View).
* The QUESTION_NUMBER field is usually not usable when LEFT_ITEM_TEXT has been styled with regards to position, but you will see this immediately when previewing the CRF. If you need the QUESTION_NUMBER, an option is to include it in the LEFT_ITEM_TEXT, but keep in mind that the QUESTION_NUMBER text will always be left justified.
# Perl Programming/Keywords/eval
## The eval keyword

There are two uses of this keyword. The first form is the so-called "string eval" and executes the EXPRESSION as it were a Perl program. The second form, the code within the BLOCK is parsed once together with the code surrounding the eval itself, and executed within the current Perl program context. This form is typically used to trap exceptions more efficiently than the first, and also checking the code within BLOCK during compile time.
# Perl Programming/Keywords/else
## The else keyword

else is the keyword used to add an unconditional branch to an if … [end if] … statement.

### Syntax
## See also

* Conditionals
# Perl Programming/Keywords/eq
## The eq keyword

eq is a relational operator that returns 1 for true, if the lefthand side is stringwise equal to the righthand side, and an empty string ̈("") for false.
# Perl Programming/Keywords/exists
## The exec keyword

exists returns true, if an expression that specifies an element of a hash exists, and the specified element in the hash has been initialized to any value (like undef).
Although exists can be called on arrays also, its behaviour strongly depends to the use of delete on arrays, having a much less clear behaviour.

### See also

* system
# Perl Programming/Keywords/elsif
## The elsif keyword

elsif is the keyword used to add another conditional branch to an if statement. The keywords else if do the same.

### Syntax
## See also

* Conditionals
# Perl Programming/Keywords/exec
## The exec keyword

exec executes a system command and quits the Perl program. To return back, system should be used. The only way exec returns, if the command does not exist and it is executed directly instead of via your system's command shell. In this case, it fails and returns false.

### See also

* system
# Perl Programming/Keywords/eof
## The eof keyword

eof is a function that returns 1 for true, if the next read over the file handle will return an end-of-file, or the file to be accessed by FILE_HANDLE is not open.
# Perl Programming/Keywords/exit
## The exit keyword

exit finishes the execution of the program after valuating EXPRESSION. It returns with this value.
Although exists can be called on arrays also, its behaviour strongly depends to the use of delete on arrays, having a much less clear behaviour.

### See also

* die
# Perl Programming/Keywords/exp
## The exp keyword

exp returns exponent e to the power of EXPRESSION. If EXPRESSION is omitted, exp($_) is executed.

### See also

* log
# Perl Programming/Keywords/for
## The for keyword

for is the keyword used to start a for loop.

### Syntax
## See also

* Control flow
# Pinyin/Pancreas

Pancreas is an organ that makes hormones and enzymes to help digestion. Pancreas helps break down carbohydrate, fat, and protein. Pancreas is at the left side of the human body and behind the stomach.
yirzahng shih zhihzaoh hormone her meirsuh yii bangzhuh xiaohuah d qihguan. yirzahng bangzhuh jieehuah tahnshuiiwuh, zhifarng, her dahnbairzhih. yirzahng zaih rerntii zuoomiahn, weihbuh houhmiah.
# Pinyin/Pair

See also
# Pinyin/Parent

A parent is a person's father or mother.
fuhmuu shih fuhqin huoh muuqin.
# Permaculture Design/Edible plants Classification and Care

Under the three domain system,(the current standard for biological classification) All plants fall into the kingdom Plantae. Grouping edible plants in terms of their genetic clades can be very useful in establishing and predicting the care which a specific species/cultivar needs.
* Angiosperms
* Gymnosperms
# Permaculture Design/How to/Creating a natural balance
## Some main points

* Don't panic! Take your time.
* Remember the forest & how it keeps a balance. The web of life. Take a walk in one whenever you need a refresher course.
* Everything gardens.
* Observe what’s eating what & when in your garden.
* Let them eat some! What can you accept?
* Plagues are indicators of gross imbalance.
* Too many pests? No ~ too few predators , or poor plant health, or soil health, or care of plants, or selection of plants, or lack of diversity, above & below ground (of animals, plants, habitats, insects & birds)

## Respect insects we need them in our gardens

What do they do? ~ fertilise, aerate, decompose, add nutrients, provide food for birds, animals & other insects (us too if only we would try them!), prune ( tribal gardeners have used insects to increase the yields of their crops by putting insects on their plants at certain times!), destroy weak plants & so help with natural selection, help plants through symbiotic relationships.

## Plants can protect themselves

Some secrete enzymes when chewed which affects the insects digestion &/or their ability to reproduce. Others produce chemicals which smell like the alarm signals put out by insects being eaten. Trees in Africa being eaten by animals send signals to neighbouring trees & those trees secrete substances that make them unpalatable!
* Create a seed bank in your soil. Let plants spread their seed & select the strongest.
* Use your own instincts to help you to see what’s needed in your garden.

## Some plants to encourage predators

* Let carrot, radish, parsnips, fennel & brassicas flower, even if you aren’t collecting seed.
* Phacelia tanacetifolia, (Fiddleneck),Solidago canadensis (Goldenrod), Asters (Michmaelmas or Easter Daisy) Alyssum maritimum (Sweet Alice) all supply nectar for predators.
Generally introduce as many flowering plants into, &/or plant them around your garden. Do some research to work out which one’s to plant to extend the flowering season.
Spraying with even botanical sprays should be a last resort as these too can kill your beneficial insects.

## Some design strategies

* Sun~trap hedge, repellant or attractant.
* Camouflage plantings.
* Clump plantings rather than rows.
* Trees & shrubs as flight barriers & wide (1/2 ~ 1mtr) rows of repellant plants
* Create habitats ~ ponds, perches, shelters, warm, wind free micro climates.

## Further reading

* The Wilderness Garden ~ Jackie French
* Organic Plant Protection ~ Rodale Press, Inc.
* Permaculture Home Garden ~ Linda Woodrow
* Organic Gardening ~ Peter Bennett.
* Natural Gardening & Farming in Australia (Don’t be put off by the “in Australia” bit; it’s applicable anywhere.)
# Permaculture Design/How to/Effective but non toxic sprays
## Water

* pressure knocks insects off.
* with lime added & applied around beets & cabbage, scab,
* clubroot & cabbage is reduced.
* Warm 54deg. C. for soft skinned insects, aphids & caterpillars.

## Milk

* control sprays on tomatoes, cucumber & lettuce. Spray at planting time & then every 10 days, 1 part milk to 9 parts water.
* Buttermilk is good for red spider mites. Add1/2 teacup b’milk to 4cups flour & 5gal. water.( an old recipe!)

## Soap

* dissolve 2 tsp pure soap e.g. LUX, in 1lt water (you can use old soapy water from washing clothes), or use soft soap not ordinary soap (caustic soda) & dissolve 225gr in 9lt water. For aphids, white butterfly & caterpillars.

## Ground rock dust

* mix water, flour & soap & sprayed on leaves. Deters soft bodied insects as sharp.

## Crushed clay

* dust on to repel caterpillars.

## Vege cooking oils

* paint on or mix with water to spray on for aphids, whitefly & mealy bugs.

## Fish emulsion

* repels many insects & fertilises plants.

## Other methods

* Wormwood cuttings put them over brassicas to camouflage & repel.
* Give plants susceptible to whitefly, comfrey liquid or use the leaves as a mulch & in your compost. Whitefly occurs when potash levels are low. Wood ash & rock phosphate also helps.
* You will see that you will need nozzles on your sprayer that can cope with the thicker mixes. They need to be used quickly, not stored.These sprays work by various means ~ smothering, deterring & dissolving insects protective shells.

## References

Thanks to Tania J. McLean, Waitati & Rodale Press U.S.A.
# Permaculture Design/How to/Planting Calendars

At this stage, these planting Calendars are intended to help new comers to an area start planting productively. In that regard, the plants listed are common, generally well known, tested by many in that area. If you would like to develop a plan for your area, introduce yourself to a planting community and make notes on what they say. Start your calendar here and help us build plans for many regions.
* Dunedin New Zealand
* Darwin Australia
# Permaculture Design/How to/Planting Calendars/Darwin Australia
## March

* Sow herb seeds in large pots
* Sow seeds for dry season plants in shade house
* Capsicum seeds in large pots
* Seed tomato in large pots in shade. Toms to avoid pests
* Cucumber seeds directly into beds, and replant each month
* Prep beds and renew mulch ready for dry season
* Fertilise crops that go dormant in the dry season, such as ginger, turmeric, and caladium
* Fertilise fruit crops for strong growth through the dry season
* Check or install irrigation system for dry season
* Prune mulberry and guava
* Cut back eggplant, okra and chillies, fertilise to encourage regrowth
* Cut off yam bean flowers to direct energy to tubers
* Take cuttings from a strong dragon fruit that is older than one year

## April

* Begin to plant out dry season crops
* Sow cherry tomato seeds in seedling pots under shade. Plant out when weather starts to cool
* Coriander seeds directly into ground. Sow again each month to keep fresh leaves. Allow older pants to flower to encourage insects
* Mulch beds heavily
* Continue to shade seedlings
* Break flowers off banana bunches if fully formed, and fertilise heavily
* Clean irrigation system
* Thin out 3 year old bamboo
* Continue to build up compost, and liquid compost ready for the dry season
# Proteomics/Protein - Protein Interactions
### Presentation

| Post-translational Modification | Protein - Protein Interactions | Protein Chips | List of Topics | Protein Chips |
Chapter edited and updated by: Poulami Barman and Sarah Allen
Contact pxb2979@rit.edu, sea3016@rit.edu

## Introduction

Protein interaction is crucial for every organism. Most proteins function through interaction with other molecules, and often with other proteins. Enzymes interact with their substrates, inhibitors interact with enzymes, transport proteins interact with structural proteins, hormones interact with receptors – and that’s just a few of the interactions that happen in a cell. Some proteins are composed of more than one polypeptide chain, and the interactions between the different peptides are necessary for the whole protein to function. Since they are so essential, protein-protein interactions are an important topic for scientists to understand.
There are many characteristics of a protein-protein interaction that are important. Obviously, it is important to know which proteins are interacting. In many experiments and computational studies, the focus is on interactions between two different proteins. However, you can have one protein interacting with other copies of itself (oligomerization), or three or more different proteins interacting. The stoichiometry of the interaction is also important – that is, how many of each protein involved are present in a given reaction. Some protein interactions are stronger than others, because they bind together more tightly. The strength of binding is known as affinity. Proteins will only bind each other spontaneously if it is energetically favorable. Energy changes during binding are another important aspect of protein interactions. Many of the computational tools that predict interactions are based on the energy of interactions.
In recent years there has been a strong focus on predicting protein interactions computationally. Predicting the interactions can help scientists predict pathways in the cell, potential drugs and antibiotics, and protein functions. However, it has been an ongoing challenge to decipher those interactions. Proteins are large molecules, and binding between them often involves many atoms and a variety of interaction types, including hydrogen bonds, hydrophobic interactions, salt bridges, and more. Proteins are also dynamic, with many of their bonds able to stretch and rotate leading to different conformations. Therefore, predicting protein-protein interactions requires a good knowledge of the chemistry and physics involved in the interactions.
This chapter discusses the characteristics of protein-protein interactions, how they are determined experimentally, and how they are predicted computationally. It also contains a list of databases where you can explore known and predicted protein interactions. The links above will lead you to the various sections.