From ClothoWiki

Contents 1 FAQ 1.1 Basics 1.1.1 Question: What do I need to run Clotho? 1.1.2 Question: Does Clotho run on a Mac? 1.1.3 Question: How do I figure out what version of Java I have? 1.1.4 Question: Does Clotho run on Linux? 1.1.5 Question: Do I need Netbeans to run Clotho? 1.1.6 Question: How do I set up a database to use with Clotho? 1.1.7 Question: How do I get more information or submit a question? 1.2 How Do I... 1.2.1 Question: How do I change the current user? 1.2.2 Question: How do I see who the current user is? 1.2.3 Question: I forgot my password. How do I reset it? 1.2.4 Question: How do I delete information I have saved to the database? 1.2.5 Question: How do I find a Part with a given sequence? 1.2.6 Question: The start and stop codons get chopped off my Features, how do I get them back? 1.2.7 Question: How do I add a new Format? 1.3 Specific App Questions

This page should serve as a discussion platform for Clotho users in the form of questions and answers. Be sure to check out the forum at http://www.clothocad.org if you question is not found here. The most frequently asked questions from the forum will be migrated here. Also check out the Developer FAQ as well.

FAQ

Basics

Question: What do I need to run Clotho?

Java 6 is the primary requirement. Inherently to have Java 6 you will need things like a functioning computer, up to date OS (i.e. not Windows 3.1), a keyboard, etc.

Question: Does Clotho run on a Mac?

Yes provided that you have Java 6 installed. Java 6 may not be available for older versions of Macs. Try this and see if it solves the problem:
Go to spotlight and type in java. Open the application called "Java Preferences." On the lower section of the box that pops up, called Java Applications, there is a box with Java versions in it. Drag Java SE 6 to the top.

If you don't have Java 6 installed on your Mac:

1. Install the JDK 6
Without the JDK 6, Clotho will prompt that the application cannot run under other versions than JDK 6 
and tell the user to download JDK 6 on the official website, which is www.oracle.com.

However, the oracle doesn't provide JDK 6 for Mac. What users need to do is download it from apple. 

Google "Java for Mac OS X <version> Update" where <version> should be replaced by the current version of the the user's Mac OS X.


2. Set the default version of JDK to 1.6.
The update installation may not do this automatically. 

There are two ways achieving so:
First, we can go to Application--> Utilities--> Java Preferences --> Drag "Java SE 6" on the top preferences. 

Alternately, you can use the Terminal.
Go to the directory by typing cd /System/Library/Frameworks/JavaVM.framework/Versions
Set the current JDK as 1.6 by typing command:
sudo ln -fhsv 1.6 CurrentJDK
Then you need to enter your Mac's password. 
After this is done. We can use following command to verify:
java -version
Similar information will appear like this:
java version "1.6.0_22"
Java(TM) SE Runtime Environment (build 1.6.0_22-b04-307-9M3263)
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03-307, mixed mode)

Question: How do I figure out what version of Java I have?

The simple answer is to go to a command prompt and type "java -version".

Question: Does Clotho run on Linux?

Question: Do I need Netbeans to run Clotho?

You don't need Netbeans to run Clotho. You do need Netbeans however to develop new apps for Clotho.

Question: How do I set up a database to use with Clotho?

See Database Setup for specifics. Remember that you have three options regarding how to run Clotho: use the local connection (save data to a local file; really just for trying Clotho out), use a 3rd party service (someone else hosts your data), or set up your own database. Naturally there is a 4th option: use another lab's Clotho database provided that they give you the login information.

Question: How do I get more information or submit a question?

First of all start by checking the FAQs on this site. Then check out the forum at http://www.clothocad.org and post a question. If all else fails here are some other options:

For general information or to contribute (not bug reports): clothodevelopment AT googlegroups DOT com

For emails regarding any bugs (not general questions): clothobugs AT googlegroups DOT com

For emails regarding any desired features (response time varies): clothofeatures AT googlegroups DOT com

For emails regarding app (plugin) developments (not bugs): clothoplugins AT googlegroups DOT com

If you wish to get updates on Clotho's status, updates, etc, please join: clotho-users AT googlegroups DOT com at http://groups.google.com/group/clotho-users

How Do I...

Question: How do I change the current user?

There are many ways...it can be done using the Groovy Scripter, and additional tools may provide this function. However, the most convenient route is the Dashboard. While it's in focus, type control-U, and it will allow you to choose yourself and enter your password.

Question: How do I see who the current user is?

The only way to do that with the tools currently installed on the downloadable version of Clotho is through the Groovy Scripter. However, it would be fairly easily to implement that in a Clotho app. While connected to the database, launch Groovy Scripter, paste in the code below, type control-R, and Person Editor should pop up with the current user.

Collector.getCurrentUser().launchDefaultViewer();

Question: I forgot my password. How do I reset it?

Question: How do I delete information I have saved to the database?

In Clotho 2.0, this is not available. However, this will become available in the next release. For now, just remove things you don't want from your Collections, and they are out of sight and out of mind. If you really must remove something, you can directly access the raw data in your database using a tool outside of Clotho such as Toad, but that will take some figuring out.

Question: How do I find a Part with a given sequence?

The little white search box on the Dashboard provides this and many other searching functions. Check out the Dashboard help for more details. Briefly, let's say you want to find a Part that contains the sequence "AAAAGGA". Type "Part seq AAAAGGA" into the Dashboard and click enter. Your search will pop up a window with all the Parts containing that sequence.

Question: The start and stop codons get chopped off my Features, how do I get them back?

Clotho considers that Features encoding polypeptides are the same protein regardless of whether the start and stop codons are present or not. So, when you use a tool like Spreadit Features or Bulltrowell to enter Features, Clotho will chop off the start and stop codons if you explicitly put them in. However, when you later use autoannotation to locate Features in a sequence, Clotho will add the start and stop codons back onto the annotation if they are present. In doing so, Clotho considers ATG, GTG, and TTG as all being valid start codons and TAG, TAA, and TGA as valid stop codons. Let's say, however, that you are explictly trying to encode something like GTGAAACCC and that exact peptide with a valine at the first position is going to be used for fusion proteins. When you make that Feature, the first codon will get chopped off. However, using a Feature editing tool like Spreadit Features, you can manually add that codon back -- Clotho doesn't prevent you from starting a coding sequence with a start codon, it just trims them when you create them. when you later go to autoannotate things, you'll only get a match if the valine is present, and if there is another start codon upstream of the sequence, it will include that in the annotation. Note that you can also manually edit your annotations if they aren't the way they should be.

Question: How do I add a new Format?

Specific App Questions