|
Access Filter Strip
|
Previous |
The "Assess Filter Strip" pull-down menu allows the user to compute a new filter strip width under the changed climate scenario that has the same level of effectiveness (in terms of sediment yield) as did the original filter strip width under the original climate


OpenLayers Example
Demonstrate a simple offline map with an overlay that includes layer switching controls.


Applied XML Conference Sessions Chosen
Here. Not only were there 4x the number of sessions submitted that could be accepted, but the quality bar was so high that it was almost impossible to narrow them down. The good news for attendees is that the ones we picked are going to rock.
The seating for Applied XML is limited and all previous DevCons have sold out, so you may want to grab your seat now. And once you’ve done that, please spread the word! The more XML and web services zealots in one place, the better!


An R interface to the 'SciDB' array database <http://scidb.org>.
| Version: | 2.0.0 |
| Depends: | R (≥ 3.0.0), bit64 |
| Imports: | curl, data.table, digest, methods, openssl |
| Suggests: | Matrix, knitr (≥ 1.8) |
| Published: | 2017-04-14 |
| Author: | B. W. Lewis [cre, aut], Alex Poliakov [aut] |
| Maintainer: | B. W. Lewis <blewis at illposed.net> |
| BugReports: | https://github.com/Paradigm4/SciDBR/issues |
| License: | AGPL-3 |
| Copyright: | Paradigm4, Inc. |
| URL: | http://paradigm4.github.io/SciDBR |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | scidb results |
| Reference manual: | scidb.pdf |
| Vignettes: |
scidb |
| Package source: | scidb_2.0.0.tar.gz |
| Windows binaries: | r-devel: scidb_2.0.0.zip, r-release: scidb_2.0.0.zip, r-oldrel: scidb_2.0.0.zip |
| OS X binaries: | r-release: scidb_2.0.0.tgz, r-oldrel: scidb_2.0.0.tgz |
| Old sources: | scidb archive |
Please use the canonical form https://CRAN.R-project.org/package=scidb to link to this page.


404 - Page Not Found
You may not be able to visit this page because of:
-
An out-of-date bookmark/favorite.
-
A search engine that has an out-of-date listing for this site.
-
A mistyped address.
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You have no access to this page.
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The requested resource was not found.
An error has occurred while processing your request.
Please try one of the following pages:


--- layout: page title: Newsletter permalink: /newsletter/ categories: [] tags: [] status: publish type: page published: true ---


The quick fix suggests to split such statements into nested try-with-resources statements.
Example of try statement with multiple resources:
try (FileInputStream in = new FileInputStream("in.txt");
FileOutputStream out = new FileOutputStream("out.txt")) {
/*read and write*/
}
The example above is transformed into the following:
try (FileInputStream in = new FileInputStream("in.txt")) {
try (FileOutputStream out = new FileOutputStream("out.txt")) {
/*read and write*/
}
}


SceneJS
- Controlling FPS
Use the up and down arrow keys to increase or decrease FPS.
Current FPS:
60


{% extends "container.html" %} {% block title %} FreeJournal {% endblock %} {% block container_content %}
FreeJournal is a decentralized system for publishing documents. A document can be any type of file. These files are organized in "collections," which group the files under a common title.
Using the FreeJournal web interface is super easy. To see available documents in a collection, click the link for that collection.
You can then click a document title to download that document.
Sometimes it takes a while for a collection or document to appear on the FreeJournal web interface once it has been submitted. Large documents can take an especially long time.
{% endblock %}


Confirm unregistration
You are in the process of unregistering from this game jam.
Notice that you will leave your current team. If there is no
user left in that team, it is PERMANENTLY DELETED,
including all games, invitations and other team-related
data.
You can register again, but the data will be gone. You may have to
enter everything again.
{{ form.confirm(style="max-width:20px;max-height:14px;") }}
{{ form.confirm.label.text }}


(PECL mysqlnd_ms < 1.6.0)
mysqlnd_ms_xa_gc — Garbage collects unfinished XA transactions after severe errors
Garbage collects unfinished XA transactions.
The XA protocol is a blocking protocol. There exist cases when servers participating in a global transaction cannot make progress when the transaction coordinator crashes or disconnects. In such a case, the MySQL servers keep waiting for instructions to finish the XA transaction in question. Because transactions occupy resources, transactions should always be terminated properly.
Garbage collection requires configuring a state store to track global transactions. Should a PHP client crash in the middle of a transaction and a new PHP client be started, then the built-in garbage collection can learn about the aborted global transaction and terminate it. If you do not configure a state store, the garbage collection cannot perform any cleanup tasks.
The state store should be crash-safe and be highly available to survive its own crash. Currently, only MySQL is supported as a state store.
Garbage collection can also be performed automatically in the background. See the plugin configuration directive garbage_collection for details.
Note: Experimental
The feature is currently under development. There may be issues and/or feature limitations. Do not use in production environments.
connection
A MySQL connection handle obtained from any of the connect functions of the mysqli, mysql or PDO_MYSQL extensions.
gtrid
Global transaction identifier (gtrid). If given, the garbage collection considers the transaction only. Otherwise, the state store is scanned for any unfinished transaction.
ignore_max_retries
Whether to ignore the plugin configuration max_retries setting. If garbage collection continuously fails and the max_retries limit is reached prior to finishing the failed global transaction, you can attempt further runs prior to investigating the cause and solving the issue manually by issuing appropriate SQL statements on the participants. Setting the parameter has the same effect as temporarily setting max_retries = 0.
Returns TRUE
if garbage collection was successful. Otherwise, returns FALSE


@Synchronized public interface CommunicationRegistration extends Mutex
It composites ReceivePipeline
to handle specific Objects.
Those can be accessed by stating:
CommunicationRegistration registration = ...
ReceivePipeline pipeline = registration.register(MyObject.class);
Those pipelines
handle received Objects. You may freely register any of the following Interfaces:
All of those are a subtype of the ReceiveFamily
.
The instantiation of this CommunicationRegistration is limited to internal Developers.
trigger(Class, Connection, Session, Object)
,
ReceivePipeline
| Modifier and Type | Method and Description |
|---|---|
void |
addDefaultCommunicationHandler(OnReceive<Object> defaultCommunicationHandler)
Sets an
OnReceive as the default handling routine for any Object that is not registered specifically |
void |
addDefaultCommunicationHandler(OnReceiveSingle<Object> defaultCommunicationHandler)
Sets an
OnReceiveSingle as the default handling routine for any Object that is not registered specifically |
void |
addDefaultCommunicationHandler(OnReceiveTriple<Object> defaultCommunicationHandler)
Sets an
OnReceiveTriple as the default handling routine for any Object that is not registered specifically |
void |
clear()
Clears all set registration.
|
void |
clearAllEmptyPipelines()
This call wil unregister all
ReceivePipeline if the ReceivePipeline.isEmpty() call returns true. |
static CommunicationRegistration |
create()
Creates an instance of the CommunicationRegistration.
|
boolean |
isRegistered(Class clazz)
Determines whether or not a
ReceivePipeline is registered to handle Objects of the same Type as clazz |
List<OnReceiveTriple<Object>> |
listDefaultsCommunicationRegistration()
Lists all set DefaultCommunicationHandlers
|
Map<Class,ReceivePipeline<?>> |
map()
Creates a Map that maps the internally maintained
ReceivePipeline to the Class they have been Registered with. |
<T> ReceivePipeline<T> |
register(Class<T> clazz)
Sets/maintains a ReceivePipeline to handle a given Object of the provided Class.
|
<T> void |
trigger(Class<T> clazz,
Connection connection,
Session session,
Object o)
This method takes a Object and runs it through a
ReceivePipeline of the Type that is defined by the provided Class. |
<T> void |
trigger(Connection connection,
Session session,
Object object)
This method is used to trigger a
ReceivePipeline , with the provided arguments. |
void |
unRegister(Class clazz)
Removes the internally set instance of the
ReceivePipeline , handling an Object of the same
Type as the provided clazz . |
void |
updateBy(CommunicationRegistration communicationRegistration)
This call will override any internally set registrations and set all registration to the provided CommunicationRegistration.
|
@APILevel static CommunicationRegistration create()
It utilizes the package-private instance, located within the same package of this interface.
<T> ReceivePipeline<T> register(Class<T> clazz)
Because of type-erasure, the type check has to be done at runtime.
You will never get an receivePipeline
of another type
T
- the Type of the Object, identified by the provided Classclazz
- the Class of the Object, that should be handled.ReceivePipeline
void unRegister(Class clazz)
ReceivePipeline
, handling an Object of the same
Type as the provided clazz
.
This will ignore any ReceivePipelineHandlerPolicy
set to
the maintained ReceivePipeline
. It will simply remove the set instance.
clazz
- the Class, that defines the type of the ReceivePipelineboolean isRegistered(Class clazz)
ReceivePipeline
is registered to handle Objects of the same Type as clazz
clazz
- the Class, that defines the type of the ReceivePipeline
ReceivePipeline
is set, false otherwise@Asynchronous <T> void trigger(Connection connection, Session session, Object object) throws CommunicationNotSpecifiedException
ReceivePipeline
, with the provided arguments.
All it does, is to call trigger(Class, Connection, Session, Object)
, with the direct Class of the provided
Object
T
- the Type of the ReceivePipeline
connection
- the Connection
over which the Object was receivedsession
- the Session
, identifying the other end of the Connection
object
- the Object that was receivedCommunicationNotSpecifiedException
- if no ReceivePipeline is set for the provided class and no
DefaultCommunicationHandler is settrigger(Class, Connection, Session, Object)
@Asynchronous <T> void trigger(Class<T> clazz, Connection connection, Session session, Object o) throws CommunicationNotSpecifiedException
ReceivePipeline
of the Type that is defined by the provided Class.
This method provides the possibility to define other Class-Types than the Object is of. This is due to inheritance.
If you want to run an Object through this CommunicationRegistration, but you want it to be handled by an
ReceivePipeline
, that only handles the super type or an declared/inherited interface, you may
do that.
By calling this Method, you are basically running the provided Object through the internally maintained ReceivePipeline
.
The other provided parameters (connection
, session
) will be needed regardless of the
internally set handlers. This is because the ReceivePipeline does not know whether any set Handler needs those
parameters or not. It only knows OnReceiveTriple
To ensure scalability, this Method extracts the actual run of the ReceivePipeline
into another Thread.
Therefor this method does not rethrow thrown Errors, Exceptions and RuntimeExceptions, thrown by the ReceiveHandler.
If no ReceivePipeline
was ever registered to this CommunicationRegistration, it will throw an
CommunicationNotSpecifiedException
. his behaviour can be overridden by providing an DefaultCommunicationHandler
with addDefaultCommunicationHandler(OnReceive)
T
- the Type of the ReceivePipeline
clazz
- the Class, defining the Type of the ReceivePipeline
connection
- the Connection
, over which the Object has been receivedsession
- the Session
, identifying the other end of the Connection
o
- the Object, that was received over the Connection
CommunicationNotSpecifiedException
- if no ReceivePipeline
is set for the provided type
and no DefaultCommunicationHandler has been set.OnReceiveTriple
,
Wrapper
void addDefaultCommunicationHandler(OnReceiveSingle<Object> defaultCommunicationHandler)
OnReceiveSingle
as the default handling routine for any Object that is not registered specificallydefaultCommunicationHandler
- the OnReceiveSingle
that should be run, if no registration was found for
a specific provided Objectvoid addDefaultCommunicationHandler(OnReceive<Object> defaultCommunicationHandler)
OnReceive
as the default handling routine for any Object that is not registered specificallydefaultCommunicationHandler
- the OnReceive
that should be run, if no registration was found for
a specific provided Objectvoid addDefaultCommunicationHandler(OnReceiveTriple<Object> defaultCommunicationHandler)
OnReceiveTriple
as the default handling routine for any Object that is not registered specificallydefaultCommunicationHandler
- the OnReceiveTriple
that should be run, if no registration was found for
a specific provided Objectvoid clear()
This Call will ignore the set ReceivePipelineHandlerPolicy
.
All internally set ReceivePipeline
will be cleared.
Currently running Handlers will NOT be stopped.
void clearAllEmptyPipelines()
ReceivePipeline
if the ReceivePipeline.isEmpty()
call returns true.
The one exception for this rule is, if an ReceivePipeline
is sealed.
Any sealed ReceivePipeline
will not be tested and therefor not removed, even if they are empty.
This ensures that critical empty ReceivePipeline
are not collected.
void updateBy(CommunicationRegistration communicationRegistration)
This will ignore any ReceivePipelineHandlerPolicy
and delete all
Registrations currently set.
This CommunicationRegistration will take all instances from the provided CommunicationRegistration!
This means, both are now nearly identical! A change at one ReceivePipeline
in any of those CommunicationRegistrations
will lead to the same change in the other CommunicationRegistration!
communicationRegistration
- the CommunicationRegistration, that will provide its Registration.Map<Class,ReceivePipeline<?>> map()
ReceivePipeline
to the Class they have been Registered with.ReceivePipeline
that handles this Type or any subtypeList<OnReceiveTriple<Object>> listDefaultsCommunicationRegistration()
addDefaultCommunicationHandler(OnReceive)
,
addDefaultCommunicationHandler(OnReceiveSingle)
,
addDefaultCommunicationHandler(OnReceiveTriple)
Copyright © 2018. All rights reserved.


Online Security
online security also known as internet security is a very vast topic with a lot to cover. even if the online world is an amazing place to explore and easily accessible to anyone, there are some risks associated with it. Its good to know who your are dealing with or what you’re getting into. cyber criminals will try to take advantage of unwary visitors. Internet security encompasses browser security, the security of data entered through a Web form, and overall authentication and protection of data sent via Internet Protocol.
Computer networks hold valuable and often protected, private information, not least data on identities; credit cards; financial data; technical, trade, and government secrets; mailing lists; medical records; and the list could be continued. These data are vulnerable on the computer and in transit. The Internet, as a connector between computer systems, is also a highway of access to valuable data stores.
The vulnerabilities are loss of data through malicious erasure, the acquisition of proprietary information, the manipulation of the data such as illegal withdrawals and transfers of funds, the capture and criminal use of credit cards or identities, and any and all unauthorized uses to which information may be put. Internet security breaches can also potentially have direct physical consequences if the wrong people hijack systems that control transportation or power systems. Computers have become so pervasive, and their networking so universal, that Internet security and security in general are closely linked objectives of society.
The most important actions that one can have in mind is 1) disciplined use of computer systems including careful password and e-mail control, 2) installation and upgrading of firewalls between internal networks and the Internet, 3) alertness to news stories about new viruses and breaches and 4) prompt reporting of breaches to the authorities as soon as they are detected.


--- layout: post title: Rewriting history date: 2012-01-07 21:48:02.000000000 -08:00 type: post published: true status: publish categories: tags: [] meta: _edit_last: '1' author: login: admin email<EMAIL_ADDRESS>display_name: admin first_name: Carina C. last_name: Zon ---
Ever commit to repo and then belatedly realize that the authorship metadata isn't what it should be? Easy to do when pair programming.
Here's a nifty little script for fixing authorship of commits within a Git repository. It uses a Git plumbing command called filter-branch.
Consider the GitHub-provided script a starting point for your own, rather than a copy/paste solution. Read filter-branch's documentation carefully before using. filter-branch changes the SHA-1 value of any commits affected, which means that every descendant commit's SHA-1 will also be re-written. Of course, there are also the usual caveats about the pitfalls of changing history on a shared repo.
More info: rewriting history from Scott Chacon, in Pro Git.


We are a group of GPU experts teamed up with data scientists to bring machines to the business that want to ride the data wave. We are our original customers, we designed these machine to help us provide A.I. and deep learning solutions to our customers. So if you need help getting started or improving your current endeavor let us know.
The MachineWater Cooled NVIDIA's. We can put a range from 1 to 4 gpu's. Experience tells us 3 is ideal for a deep learning developer.
Cuda, Python 3, Keras, TensorFlow, Theano, Torch, pyTorch and more. Looking for something particular? Contact us, and we will do our best to help out.
We assemble the machine, install the software you need, and ship it to you.
We tailored these machines to be ideal for doing deep learning on multi-GPUs. Enough RAM, 500 GB SSD and 2 - 3TB hard drive to keep your data safe.
Ready to start your next Deep Learning project? Let us help you get started with the right gear. Send us an email and we will get back to you as soon as possible!


Forcecon introduces new cooling solutions for notebooks, smartphones
by Aaron Lee, Taipei; Steve Shen, DIGITIMESTaiwan-based heat dissipation solution provider Forcecon Technology has introduced a new form of heat pipe, thermal ground plane (TGP), thickened 0.2mm for notebook and smartphone applications, according to company chairman Yao Cheng-chi.
The company has delivered its TGP devices to notebook and smartphone clients for verification, likely paving the way for volume shipments in the first quarter of 2020, Yao said.
Its initial production of TGPs will reach 200,000 units, with output to be ramped up depending on market demand, Yao added.
Since TGP products can come with a thickness of 0.2mm or even 0.1mm, the TGP-based cooling solutions boast an advantage when applied to slim consumer electronics products as compared to vaper chamber (VC)-based modules, which are now available with a thickness of 0.35mm, Yao said.
In the third quarter of 2019, Forcecon posted revenues of NT$3.564 billion (US$116.88 million), net profit of NT$117 million and gross margin of 18.3%.


Control Station
DATA CONTROL TOGGLE
Remote Mine (W.AUS) <-> Sydney
CONTROL STATION LOGS
Control Station Data Logging
WIND BARD VISUALISATION
NTN Interface
SATELLITE PATH VISUALISATION
SATELLITE PATH METRICS
Satellite Latency:
No. Satellites:
Remote Site
WIND DATA VISUALISATION
Wind Direction:
Wind Speed:
REMOTE SITE LOGS
Remote Site Data Logging


al
e
x
andre
g
ag
non
english
/
français
github
/
hackerrank
/
email
Quebecer. Computer Science student. Open Source enthusiast. My goals are simple: I strive to learn and I live to innovate. Curiosity and creativity are what fuel me throughout my existence.


|
Nakama .NET 3.5
Nakama .NET Client SDK
|
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
persist
Apple, Huawei, and Google purchase receipts in the Nakama database. This is set to true
by default in order to allow the server to detect replay attacks.SeenBefore
property to IApiValidatedPurchase
.ListSubscriptionsAsync
which returns a list of the user's subscriptions.ValidateSubscriptionAppleAsync
which returns details about a user's Apple subscription.ValidateSubscriptionGoogleAsync
which returns details about a user's Google subscription.GetSubscriptionAsync
which returns a subscription for the provided product id.countMultiple
in AddMatchmakerAsync
and AddMatchmakerPartyAsync
.ValidatedPurchaseEnvironment
has been renamed to ApiStoreEnvironment
.ValidatedPurchaseStore
has been renamed to ApiStoreProvider
.CancellationTokenSource
. These have been replaced in favor of methods that accept a CancellationToken
that were added in v3.3.SocketClosed
event taking a significant length of time or not firing at all when internet connection is lost.autoRefreshSession
from overloaded Client
constructors. This can still be customized with the base Client
constructor. This is a workaround for an internal compiler error in Unity's WebGL toolchain.IPartyMatchmakerTicket
is now received by the party leader when they add their party to the matchmaker via AddMatchmakerPartyAsync
.PromotePartyMember
to PromotePartyMemberAsync
.IUserPresence
objects were not being deserialized properly by the client as part of the IParty
object.Socket.ReceivedParty
event can now be subscribed to in order to listen for acceptance events from the leader of a closed party.null
to indicate no filters.This version starts at 2.0 to match the initial server version it supports.


filmcritic.com presents a review from staff member David Bezanson. You can find the review with full credits at http://www.filmcritic.com/misc/emporium.nsf/2a460f93626cd4678625624c007f2b46/52062df4ccf337588825686f0080bda6?OpenDocument
The End of the Affair A film review by David Bezanson - 2000
Director: Neil Jordan Producers: Stephen Woolley, Neil Jordan Screenwriter: Neil Jordan Stars: Julianne Moore, Ralph Fiennes, Stephen Rea, Ian Hart, Samuel Bound, Jason Isaacs MPAA Rating: R Year of Release: 1999
I was dragged to see THE END OF THE AFFAIR expecting another lavishly costumed, pointless period romance of the Merchant-Ivory type ... only based on Graham Greene instead of Jane Austen or E. M. Forster. The kind of movie that our wives drag us to. Instead, I was converted.
THE END OF THE AFFAIR makes a lot of serious points, and offers a very modern, psychological drama in spite of the period setting (London during World War II). Instead of being another revisionist Hollywood remake, THE END OF THE AFFAIR is the best kind of historical drama: one that reminds you that history was made of real people and their emotions --- love, pain, jealousy, and emptiness.
The film revolves around a wartime affair between Sarah Miles (Julianne Moore), the wife of a civil servant, and a writer, Maurice Bendrix (Ralph Fiennes), who becomes her jealous lover. Bendrix hires an investigator (drolly played by Ian Hart) to follow Sarah, convinced that she can't love him as purely as she does. Ultimately, he finds that the rival for her affections is not another lover, but something more unexpected.
Graham Greene, who converted to Catholicism before writing THE END OF THE AFFAIR, was one of the last generation of writers (along with contemporaries like Evelyn Waugh, C.S. Lewis, and William Faulkner) to seriously consider the implications of religious belief. Greene's refusal to resolve his ambivalent faith is transcribed in the movie, which goes deeper than the fashionable nihilism of most movies these days.
Director Neil Jordan returns to form with this work. Jordan has brought Greene's novel alive, revealing the conflicted, turbulent emotions of the survivors of the Blitz. The cast is excellent, including Fiennes as the lout and Stephen Rea as the cuckold; but Moore's sensual portrayal of Sarah, an ordinary individual forced to struggle with belief, is the most haunting, and worth an Oscar nod.
THE END OF THE AFFAIR offers a much more balanced view of faith than many supposedly religious movies --- unlike, say, THE GREEN MILE, with its unbelievable Christ-figure and obvious social-gospel message, or the whiny, cliched despair of ANGELA'S ASHES. By holding God accountable for pain and suffering as well as miracles, the makers of THE END OF THE AFFAIR capture the uncertainty and passion of people struggling with real faith.
**** 1/2 (four and one-half stars)
-- Christopher Null -<EMAIL_ADDRESS>- http://www.filmcritic.com
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


DFriday evening drinks + snacks
WSaturday wedding + reception
BSunday morning picnic brunch
Renting out an empty apartment through Airbnb is a fantastic alternative to hotels in NYC. There are usually lots of great options available in Brooklyn in the Summer, often cheaper and more convenient than hotels. Some Brooklyn neighborhoods we recommend are Greenpoint, Williamsburg, Brooklyn Heights, Cobble Hill, Boerum Hill, Gowanus, Park Slope, Prospect Heights, and Fort Greene. Also check out Long Island City (right over the river in Queens).
If you have a larger group, VRBO (HomeAway) is another great option for renting out larger houses and apartments throughout the city. This may also be cheaper and more comfortable than a hotel.
If you’re looking for a hotel, here are a few suggestions:
NU Hotel 85 Smith St, Brooklyn, NY
NU Hotel is a great option if you’re planning on staying for a few days. It’s in a great location (we live a couple blocks away) and is close to many subway lines.
The Box House Hotel 77 Box St, Brooklyn, NY
If you’re in Brooklyn for a short amount of time, The Box House Hotel is very close to the wedding venue. It’s further from the subway, so plan on taking cabs a bit more to get around.
Wythe Hotel 80 Wythe Ave, Brooklyn, NY
A more upscale (and trendy) option is the Wythe Hotel. It’s located in Williamsburg, surrounded by lots of restaurants and shopping. Williamsburg is in between the wedding venue and the other weekend events.
Holiday Inn Express 625 Union St, Brooklyn, NY
A wallet-friendly option, located in an up-and-coming neighborhood that keeps getting more interesting, and short cab ride from both Friday and Sunday’s events. It’s also walking distance to some great bars and restaurants.


Scriptella ETL Frequently Asked Questions
-
1. General
- 1.1. Where can I find documentation on script syntax for driver FOO/BAR/...?
- 1.2. Does Scriptella support Microsoft Access?
- 1.3. What is the difference between $variable / ${expression} and ?variable / ?{expression} syntax.
- 1.4. How to share a mutable variable between script/query elements of an ETL file?
- 1.5. How to call a static method in JEXL expression?
- 1.6. How to escape spaces in field names?
- 2. SQL
- 3. CSV/Text
1. General
1.1. Where can I find documentation on script syntax for driver FOO/BAR/...?
An up to date drivers documentation is available in the Scriptella Javadoc. Reference Documentation also covers drivers usage and scripts syntax.
1.2. Does Scriptella support Microsoft Access?
Microsoft Access and other databases with ODBC interface are supported via ODBC-JDBC bridge driver which comes with Sun's JRE. Download ODBC example for more details. Connection declaration example:
<connection url="jdbc:odbc:DRIVER={Microsoft Access Driver (*.mdb)};DBQ=Northwind.mdb"/>
1.3. What is the difference between $variable / ${expression} and ?variable / ?{expression} syntax.
Binding variables syntax varies between drivers. JDBC drivers use the following rules for properties substitution:
- $variable - inserts a value of the variable as text content.
- ${expression} - braces are used for JEXL expressions. For example ${column1+column2} inserts a sum of 2 columns.
- ?variable, ?{expression} - syntax is the same as in 2 previous examples, but the
result of evaluation is set as a prepared statement parameter, thus increasing the performance
and eliminating the need to escape values.
Please note that currently ?{} syntax is only supported by the JDBC drivers.
See Reference Manual for additional details.
1.4. How to share a mutable variable between script/query elements of an ETL file?
In general such practice in not recommended because often it's a sign of a bad design. It's like using GOTOs or global variables in programming languages. But in several cases using a global variable may help to achieve required goal. We propose 2 approaches:
- Use etl.globals map to work with global variables. Example ${etl.globals['globalVar']}
- Another approach is similar to the technique utilized in anonymous inner classes to modify a single-element array declared as a final variable.
The following example demonstrates both approaches:
<etl> <connection driver="script" id="js"/> <connection url="jdbc:...." id="db"/> <!-- Set number of records as a global variable --> <!-- Note that JEXL syntax etl.globals['globalVar'] does not work in JavaScript --> <query connection-id="db"> select count(id) as c from Errors <script connection-id="js"> etl.globals.put('errorsCount', c); <script> </query> <!-- Then reuse this variable in other parts of ETL file --> <script connection-id="js" if="etl.globals.get('errorsCount') gt 0"> java.lang.System.out.println('errors count ='+etl.globals.get('errorsCount')); </script> <!-- Alternatively an outer query can be used to share an array based variable between scripts --> <query connection-id="js"> var pseudoGlobalVar = []; //Declare pseudo-global variable available to nested element query.next(); //Executes child scripts <script> //Updates the variable pseudoGlobalVar[0] = 1; </script> <script> //Outputs updated value of global variable java.lang.System.out.println('pseudoGlobalVar[0]='+pseudoGlobalVar[0]); </script> </query> </etl>
1.5. How to call a static method in JEXL expression?
Load a class by name by using class:forName Scriptella function
Example. Call System.getProperty:
${class:forName('java.lang.System').getProperty('propName')}
1.6. How to escape spaces in field names?
You can use etl context variable ${etl.getParameter('var name')} to reference any column names.
Additionally several drivers
including CSV and JDBC allow referencing columns by an index, i.e. $1, $2 ... $n.
Example:
<query connection-id="csv"> <!-- Read CSV file content --> <script connection-id="text"> <!-- Print columns, column 2,3 are referenced by name, 1,4 - by index --> $1,$secondColumn,${etl.getParameter('My Column')},$4 </script> </query>
2. SQL
2.1. How to create an Oracle trigger (run a PL/SQL block)?
To recognize Oracle PL/SQL statement blocks you'd have to specify plsql=true connection property (supported only by Scriptella Adapter for Oracle). In this case a slash(/) on a single line is used as a statement separator:
<connection driver="oracle" ...> plsql=true </connection> <script> CREATE OR REPLACE TRIGGER secure_del_trigger BEFORE DELETE ON emp FOR EACH ROW DECLARE unauthorized_deletion EXCEPTION; BEGIN IF <your business rule is violated> THEN RAISE unauthorized_deletion; END IF; EXCEPTION WHEN unauthorized_deletion THEN raise_application_error (-20500, 'This record cannot be deleted'); END; / -- Other statements separated with a slash on a single line </script>
If you are using Oracle JDBC driver directly then set the following configuration properties:
<connection driver="oracle.jdbc.driver.OracleDriver" ...> statement.separator=/ statement.separator.singleline=true </connection>
This idea is similar to Ant solution.
2.2. How to control commit options and transactions?
The following connection parameters are supported by the JDBC bridge:
- transaction.isolation - Transaction isolation level name
- autocommit - Enables/disables auto-commit mode.
- autocommit.size - Enables/disables auto-commit mode.
If the autocommit is true, then setting autocommit.size has no effect.
Example:
<connection driver="auto" url="jdbc:hsqldb:mem:test"> autocommit.size=4 <!-- Automatically commit after every 4th statement --> transaction.isolation=SERIALIZABLE <!-- Sets TX level to Serializable --> </connection>
2.3. How to UPSERT (update or insert into a table?)
You can leverage database-specific SQL statements like MERGE or UPSERT. See answers on StackOverflow:
An alternative approach, which is universal but is typically slower, is to use count(*) statement and do insert or update accordingly:
<query connection-id="in"> SELECT * FROM Persons_In <query connection-id="out"> SELECT COUNT(*) as cnt FROM Person_Out WHERE Person_ID=?Person_ID <!-- If nothing found - insert --> <script if="cnt==0"> INSERT INTO Person_OUT VALUES (Person_ID, Person_Name, ...); </script> <!-- Otherwise - update --> <script if="cnt gt 0"> UPDATE Person_OUT SET Person_Name=?Person_Name WHERE Person_ID = ?Person_ID; </script> </query> </query>
3. CSV/Text
3.1. How to output null value as empty string in a CSV/Text file.
Suppose we have 3 variables - a='valueA';b=null and c='valueC'.
Here is a CSV script which outputs them in a single line:
$a,$b,$c
The output for this script:
valueA,$b,valueC
By default NULL variables are not substituted, because Scriptella substitution engine cannot distinguish null value from undeclared variable. This behaviour is not always desired. As a workaround you can specify a null_string connection property as follows:
<connection driver="text"> null_string=<!-- Expand nulls to empty string --> </connection>
And the output is:
valueA,,valueC


Here is the header of the INF file:
| | INF 1.0 |
| | LEVELNAME SECBASE |
| | |
| | items 2 |
INF File version and level name, followed by total number of items in the file.
Don't forget to change this value when you add or remove items in an INF.
Then follow the items:
| | item: sector name: secname |
| | seq |
| | ........ |
| | seqend |
A Sector Item.
| | item: sector name: secname num: #wallnum |
| | seq |
| | ........ |
| | seqend |
A Wall Item.
etc.
See also item: level
Each item follows the same format, structured by the seq and seqend statements, between which the definitions are contained.
Note:
More than one class statement is allowed per item.


ToolManDHTML has been inactive since 2005. I've left it up for posterity, but I no longer support it. You may fork it on GitHub.
Direct manipulation, particularly drag and drop, is under utilized in desktop applications and is almost non-existant in web applications. That's in the process of changing.
A collection of Direct Manipulation examples that work in modern browsers. Each example is a proof of concept. I'm answering the technical question "Can I do this?" as opposed to the interaction design question "Should I do this?".
Most of the JavaScript has been bundled into a reusable package called the ToolMan DHTML Library which you can download and use for free.
The dragging script was originally based on Youngpup's DOM-Drag. Sorting was originally based on Simon Cozen's Javascript drag-and-drop ordered lists.
Quirksmode has been invaluable across the board.


You may upload users as a .csv file. The .csv file must have a header
row with these columns: username
, email
,
name
, pointsToAward
, organization
,
locale
, role
.
role must be one of USER
, ADMIN
, or
PRIZE_ADMIN
.


This page is a demonstration of the File API with Drag and Drop. This works in the latest versions of all major browsers, but you may need to place this file on a web server to get it to work.
This page attempts a file upload, for which you need to set this up on a server.


Contact
If you have an issue just file it
We'd be happy if you join the development: Clone/Fork the git repository
Visit us on GitHub
Visit our homepage
{% extends 'layout.html' %} {% block title %}Contact{% endblock %} {% block content %}
If you have an issue just file it
We'd be happy if you join the development: Clone/Fork the git repository
Visit us on GitHub
Visit our homepage


Macro (not StickOtherRelativeLinks mode)
pages to be checked
Root
Sub
You can ignore the follwing block, but it would be:
“from-file” condition: false
“from-file” condition: false


This shows the d3 general update pattern (enter, exit, update), with filtering based on a form value. It also shows a nested italics element to demonstrate that data is bound to nested elements, and how there's a need to update the nested element but there is not need to explicitly remove the nested element; it's sufficient to remove the parent.
Showing values >=
Hiding values <


Section: 7 Academic Research as a Project or Approved Use
A. The Data Trust may, in this Agreement or through a future vote of the Governance Board, approve academic research as an approved use of the Trust-managed Data Resources. If approved, the Trustee shall make available a secure Data Trust Research Hub (“Research Hub”) for access by approved researchers, for approved research, and put in place a process for certifying academic researchers for access to Trust-managed Data Resources through the Research Hub. This Research Hub may be managed by the Trustee or Trustee Affiliate(s). Approved uses, including approved academic research, shall be documented under Allowable Uses of Exhibit C attached hereto.
B. Individual researchers or research institutions (“Third Party Researcher”) may submit a proposal for the use of Trust-managed Data Resources that include personal information or sensitive personal information. This proposal must be approved in writing or by electronic approval process conducted by Trustee and Governance Board.
C. Prior to accessing any data via the Research Hub or any other means, Third Party Researchers will be required to execute a Data Trust researcher agreement with the Trustee on behalf of the Data Trust that stipulates the permissions, use, and analyses approved, including timeline and publications. Further, Trustee or Trustee Affiliate(s) will provide prior written or electronic notice via Member’s electronic portal that their data will be used by such Third Party Researcher as described in the Researcher data sharing agreement. Member may notify Trustee at any time to revoke such Third Party Researcher’s access to the data.
D. Prior to being approved for access to the Research Hub, Third Party Researchers shall sign a Data Trust researcher agreement and complete a required training course which covers the use of the Research Hub, allowable use of data provided via the Research Hub, Third Party Researcher obligations to Members, ethical guidelines, reporting of accidental misuse, and research review prior to publication. This training will be detailed on the Research Hub’s website and will be updated from time to time. Proof of training completion will be required prior to the issuing of Research Hub credentials.
E. Third Party Researcher shall be required to complete relevant IRB approval prior to approval for access and use of Trust-managed Data Resources for research.
F. The Governance Board may elect to establish a Research Hub Review Committee for the purposes of reviewing and approving Third Party Researchers and their respective proposals. Governance Board representatives will nominate Data Trust Member representatives including experienced researchers or other technical experts to participate on the Research Hub Review Committee. Governance Board representatives may also nominate representatives from relevant communities or local interest groups to participate. Research Hub Review Committee members must be approved by the Governance Board.
G. The Governance Board or the Research Hub Review Committee will periodically review and approve through unanimous vote categories of allowable uses of Trust-managed Data Resources by Third Party Researchers along with their associated responsibilities and restrictions.
H. The Governance Board or the Research Hub Review Committee will review and approve proposals for new categories of research uses on a quarterly basis.
I. The Trustee will register and make publicly available all approved Third Party Researchers and proposals.
J. Data Trust Members will retain the right to opt out of the use of their member-contributed data resources in any particular research project at any time.


ProteomeCommons.org IO Framework @versionNumber
This is a free, open-source, Java framework for handling spectra and peak list files. The framework can read and write to a number of different spectra and peak list formats, and the framework provides a simple, intuitive Java object model for working with spectra or peak lists. The overall goal of this project is to make working with peak list or spectral data easy, even if you are working with various different file formats or if you are working with incredibly large files. Additionally, we aren't trying to lock developers in to using Java. Utility programs are included that will translate peak list or spectral data in to a simple, plain text format that is well-suited for passing via regular expressions in Perl, Python, VBScript, or any other programming language.
In short, the goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
You may always find a current download of this framework at http://www.proteomecommons.org/current/531/. If you'd like the source-code, please read the developer docs.
Special notice: please help us give the IO Framework a good peak picking algorithm!
- Credits
- Changes
- Known Formats
- Applied Biosystems/Sciex: .t2d, .bic, and .wiff
- Bruker: .baf, .fid, .yep, and AutoExecute runs of LCMALDI
- Mascot Generic Format: .mgf
- Proteomics Standards Initiative (PSI): mzData 1.04 and mzData 1.05
- dataXML/massSpecXML: dataXML 0.9 (beta support)
- mzXML: mzXML 1.1.1, mzXML 2.0, and mzXML 2.1
- Waters/Micromass: .pkl and .raw/ (directory structure)
- National Institute of Standards and Technology (NIST) Library of Peptide Ion Fragmentation Spectra .msp
- Plain Text: .txt
- Sequest: .dta
- Thermo Finnigan: .raw
- X!Tandem Output Files (aka TheGPM output) .xml, .thegpm.xml, .tandem.xml, .amethyst.xml, .opal.xml, .jasper.xml
- Auto-compression/decompression Support
- Pick picking algorithm - we need your help!
- Examples/Utilities
- Frequently Asked Questions
- Developer Documentation
- Links to other projects that Read/Write these files formats
- TODO List
- Licensing Information
Credits
This is a project supported and contributed to by many different people. Here is a formal list of all of those who have submitted code and/or documentation.
Primary developers and maintainers.
- Jayson Falkner -<EMAIL_ADDRESS>Code contributors, documentation contributors, and supporters.
- Neil Swainston -<EMAIL_ADDRESS>- Panagiotis Papoulias, aka Takis -<EMAIL_ADDRESS>- Tomas Pluskal
- Jarret Falkner -<EMAIL_ADDRESS>- David Hancock -<EMAIL_ADDRESS>- Dominic Battre
Support for this project, in part, comes from the National Resource for Proteomics and Pathways (NRPP).
Changes since 6.2 (@buildNumber)
- Added support for the beta version of the dataXML efforts (merge of mzXML and mzData)
Changes since 6.1 (@buildNumber)
- Disabled the GUI helper that highlights boxes. It can be enabled by right-clicking and selecting the enable option.
- Added a "Don't Convert" option. This option will cause the GUI not to convert an intermediate file. Click this option if you want to access the exact mzXML document generated by either ReAdW or CompassXport. This feature only works for those tools.
- Added a helper message to the GUI stating, "Right-click for options (exit, etc.)" as per user request.
- Added the ReduceMemoryUsageFilter class for reducing peak list information in order to save memory. This filter is handy if you are storing large amounts of peak lists in memory and you only care about m/z and intensity information.
- Fixed the new GUI to behave well on smaller screen sizes.
Changes since 6.0 (175)
- Updated the look and feel of the Peak List Conversion application.
- Added a plain-text peak list reader so that users can very easily make their own peak lists.
- Fixed the Notepad-Friendly text export to show output as expected. See docs.
- Full read/write auto-compression support for GZIP, ZIP, bzip2, and LZMA (aka 7zip's algorithm) are now available. Test cases show that they work very well.
- The RAW reading code now defaults to the well-known location described in the docs. If the GUI is running, it will prompt the user to locate ReAdW.exe.
- Refactored mzData code to properly handle different versions. Support is now implemented for versions 1.05.
- Refactored mzXML code to properly handle different versions. Near-complete support is now implemented for versions 1.1.1, 2.0, and 2.1.
- Fixed a minor bug with the MGF writer where the "+" sign would not be included after positive charges, .e.g "CHARGE=2" versus the correct "CHARGE=2+"
- DTA peaklists may now have more than one DTA in them. File names won't be correct; however, users can create the files.
- MGF to PKL and MGF to DTA conversion now works as expected.
- MGF peaklists no longer start with a blank line.
Changes since 5.0 (150)
- Big code refactor to simplify development. Developers can no longer use the memory efficient interfaces (next(), hasNext(), etc.). Now all peak list reading must be done using the getPeakList() method, which greatly simplifies the existing code and makes it much easier to include meta-information from formats such as mzXML, mzData, and MGF.
- Added support for using Bruker's CompassXport utility to allow .fid, .yep, .baf, and AutoXecute run for LCMALDI files to be read by the IO framework. Users must manually install CompassXport to use this functionality, and the CompassXport license explicitly states that users may not use it as part of a commercial product.
- Added read support for X!Tandem output files and files generated by TheGPM. These files are in an XML-compatible format.
- Added read support for the NIST '.msp' format.
- Added read support files that are GZIP compressed. The IO Framework will automatically, based on the extension, uncompress the file and pass it to the appropriate PeakListReader instance.
- Added Neil Swainston's patch that included multiple fixes for converting from .mgf to .mzData to .mgf.
Changes since 4.4 (134)
- Major updates to the documentation and styles. This is for submission of the 5.0 release as a Bioinformatics application note.
- Added support for reading WIFF files using the wiff2dta tool.
- Added support for reading RAW files using the Sashimi project's ReAdW tool.
- Fixed several typos in the list of other software project. Thanks to David Creasy for pointing these out. Also added the "Proteios Project" link.
- Small update that increases compatibility between X Tandem and generated MGF files.
Changes since 4.3 (Revision: 120)
- Rolled in Tomas Pluskal's mzData reader fixes. Some logical refactors and tweaks to generally improve reading mzData files.
- Several documentation fixes to the Java API docs.
- Added a "links" section for links to other code that can read/write mass spec file formats. This is primarily the same list David Creasy showed at the PSI workshop.
- Added read support for the RAW format using the Thermo Finnigan's DLL file. This code is in beta-stage and will be finalized in version 5.0
- Updated the documentation to properly show version and build numbers. The build.xml script now automatically sets these strings.
Changes since 4.2 (Revision: 112)
- Added beta-support for writing mzXML format. Release 5.0 will stabilize on the code.
- Changed the GUI conversion tool to report exceptions to a user. Previously, errors would be quietly ignored. Several users reported this as a source of confusion.
- Added several regression tests to ensure that the DTA, PKL, and MGF PeakListReader classes properly work.
- Fixed the DTA bug where parent mass over charge was being incorrectly calculated when converting from MGF files. Now the DTA parent mass is always the singley charged peptide's mass.
- Fixed minor bugs with the DTA and PKL peak lists readers that would sometimes omit the first peak in a peak list.
Changes since 4.1 (Revision: 67)
- Added beta-support for writing mzXML format. Release 5.0 will stabilize on the code.
- Changed the GUI conversion tool to report exceptions to a user. Previously, errors would be quitly ignored.
- Added several regression tests to ensure that the DTA, PKL, and MGF PeakListReader classes properly work.
- Fixed the DTA bug where parent mass over charge was being incorrectly calculated when converting from MGF files. Now the DTA parent mass is always the singly charged peptide's mass.
- Fixed minor bugs with the DTA and PKL peak lists readers that would sometimes omit the first peak in a peak list.
- Added reading functionality for nucleotide sequences from BLAST databases.
- Added the MissedCleavePeptideReader class that will do missed cleaves for any of the existing peptide readers.
- Added the peptide reading code that will take a series of residues and make appropriate peptides for it in. The NonspecificPeptideReader and TrypticPeptideReader classes have been added and they do the self-named functions.
- Added a pop-up box to the GUI notifying a user when conversion is complete as to avoid confusion.
- Fixed mascot reader/writer to proper keep meta-information, particularly in the case of concatenating files.
Changes since 4.0 (Minor Release 4.1)
- Updated user docs with an explicit example of converting from T2D to plain text or mzData.
- Added in the IO-T2D project libraries. Users can now read and write in Applied Biosystem's T2D format.
- Added in Jarret Falkner's mzData writing code. mzData files may now be created via the framework.
Changes since 3.0 (Major Release 4.0)
- Added support for reading any known format that is compressed in a ZIP archive. Now you can compress your peak list data and not have to worry about decompressing it before using the framework.
- Added Jarret Falkner's mzData file format support. Peak Lists and spectra in mzData format can now be read.
- Added Jarret Falkner's mzXML file format support. Peak Lists and spectra in mzXMl format can now be read.
- Simplified Reader/Writer testing. The framework now lets you specify/load custom reader and writer objects, which means it is easier than every to test your code.
- Dominic Battre's MGF reader patch has been applied. The MGF reader is now handles comments and various different uses of whitespace characters.
- Developers can now dynamically register PeakListReader and PeakListWriter objects for use with the framework.
Changes since 2.0 (Major Release 3.0)
- Added FASTA utility programs including a protein parser, a tryptic peptide parser, and a statics generator.
- Added a peak-picking framework for converting spectra in to peak lists.
- Added the peak list filtering framework, including several example filters such as an intensity normalization filter, a intensity thresholding filter, a dynamic range filter, and a multicharge deconvolution filter.
- Added full MGF read/write support, including all meta-information.
- Added full PKL write support.
- Added full DTA write support. If multiple peak lists are written, only the first is saved in the file.
- Fixed DTA reader to properly convert m/z to what a mass spectrometer would observe.
- Added utility class for streaming peak list conversion and streaming peak list printing.
- Added an Frequently Asked Questions (FAQ) to the user documentation.
- Added streaming write support for low memory environments.
- Added proper PKL read/write support.
Changes since 1.0 (Major Release 2.0)
- Added PKL read support.
- Added DTA read/write support.
- Added example code for reading/printing peak list information. The program also serves as an abstraction point for piping peak list information in to a shell script.
- Added example code for converting between peak list formats.
- Updated Java Docs and fixed several formating bugs.
Format Information
The following peak list formats are supported, to the extend documented here.
Bruker: .baf, .fid, .yep, and AutoExecute runs of LCMALDI
Read support for several of Bruker's file formats is implemented by wrapping Bruker's CompassXport tool. This tool can be freely downloaded from Bruker's site after registering and logging in -- instructions for locating the tool are provided from both IonSource and Bioinformatics Solutions Inc.. Use the following steps to make the CompassXport tool work with the IO Framework.
- Download and install the CompassXport tool. It might be tricky to find, use the instructions provided from either IonSource or Bioinformatics Solutions Inc.
- Copy CompassXport.exe to
C:/Program Files/ProteomeCommons.org/IO/CompassXport.exe
. Note, if this location doesn't contain the file the IO Framework will automatically try C:/Program Files/Common Files/Bruker Daltonik/AIDA/export/CompassXport.exe
, which is where Bruker normally installs it.
- Convert and use any of the Bruker file formats listed below.
Special Note: When using the compassXport tool from Bruker an mzXML is generated by CompassXport then converted by the IO Framework in to the desired format. If you want mzXML and you want the exact mzXML that CompassXport produces, select the "Don't Convert" option.
Read support exists for the the following Bruker file formats.
- .baf (micrOTOF, micrOTOF-Q, and ultraOTOF-Q)
- Read support exists for .baf data via exporting data using the CompassXport tool. If you have the tool installed, the IO Framework will automatically support this format.
- .yep (esquire4000, esquire6000)
- Read support exists for .yep data via exporting data using the CompassXport tool. If you have the tool installed, the IO Framework will automatically support this format.
- .fid (microflex, microflex LT)
- Read support exists for .fid data via exporting data using the CompassXport tool. If you have the tool installed, the IO Framework will automatically support this format.
- AutoXecute run for LCMALDI (autoflex II and autoflex II TOF/TOF, ultraflex II and ultraflex II TOF/TOF)
- Read support exists for AutoXecute runs for LCMALDI data via exporting data using the CompassXport tool. If you have the tool installed, the IO Framework will automatically support this format.
Mascot Generic Format .mgf
MGF file format support is based on Matrix Science LLC's generic format. Complete MGF format support is provided by this framework; however, meta-information support is not well tested.
Helpful links
Sequest .dta
DTA file format support is based on the files used by the Sequest search algorithm. Complete DTA file support is provided by this framework. Any file ending with ".dta" is treated as if it is in the sequest DTA format.
PLEASE NOTE! The IO Framework's normal behavior deviates when handling DTA files. DTA files are intended to have one peak list per file with a known charge. Tools such as Sequest assume this and might not work properly if you include multiple peak lists in one DTA file (i.e. treat it like a PKL). The IO Framework will automatically "explode" peak list files that contain more than one peak list if they are converted to DTA. You will get several files, each with one peak list, named after the original, e.g. example.dta, example.2.dta, example.3.dta, etc. If no charge information is known, you'll also get files for charge states 1 through 3, e.g. example.1.1.dta, example.1.2.dta, etc. This is done to make the default IO Framework behavior work for the majority of use cases. Note, as a developer you can toggle the setExplode(boolean)
to disable this feature.
PLEASE ALSO NOTE! DTA only handles data that includes precursor ion information, i.e. MSMS, MSMSMS, etc. but not MS. The default behavior of the DTA writer is to ignore MS peak lists. Developers can change this at runtime by setting the setIgnoreMS(boolean)
flag.
Helpful links
Waters/Micromass .pkl and .raw (directory structure)
Waters uses two formats to represent mass spectrometry data via the MassLynx program. The .raw/ directory structure represents various forms of the raw data coming from a mass spectrometer. The .pkl format is a plain-text file containing one or more centroided, monoisotopic peak list of a .raw/ directory structure.
Phil Andrews, University of Michigan, through collaboration with Waters has implemented a free-to-use Java library for the IO Framework that can read all of the Waters file formats. Waters has shown great support for the IO Framework and our efforts to provide free support to the proteomics community for reading mass spec file formats. If you appreciate our efforts to support the Waters file formats, please take time to Waters -- thanking your Waters sales rep is likely the best way to let the higher-ups know.
Special thanks to Ronan O'Malley and James Langridge at Waters.
Please note: the Waters .raw/ directory structure support is still considered unstable and is not part of the default IO Framework releases. Please contact<EMAIL_ADDRESS>if you'd like to use this beta code.
PKL file format support is based on Micromass's PKL file format. Complete read and write support for the PKL format is implemented, including multiple peak lists in a single file.
PLEASE NOTE! PKL only handles data that includes precursor ion information, i.e. MSMS, MSMSMS, etc. but not MS. The default behavior of the PKL writer is to ignore MS peak lists. Developers can change this at runtime by setting the setIgnoreMS(boolean)
flag.
Helpful links
Plain Text
Plain text (.txt) is not really a MS or MSMS data format, but it is often what you want when manipulating data by hand. Full support exists for both reading and writing peak lists in plain-text format, e.g. you can readily export a .raw file to a tab-delimited file that you can view in a text editor. Specialized support existing for both MS Windows and non-Windows users, particularly support for people who want to look at spectra in notepad.
The plain-text format follows these three rules for both the reader and writer:
- If it is MSMS data the first line contains three tab-delimited values: the precursor ion's m/z, intensity, and charge.
- Each peak is saved on its own line with the following two tab-delimited values: fragment m/z and intensity.
- The normal plain-text writer delimits newline using just the "\n" character. The notepad-friendly plain-text writer delimits newline using the "\n\r" character combo. See wikipedia's writeup for why this helps Windows users.
Here is an example of what a peak list with a precursor m/z of 1000, a intensity of 2200, and a charge of 1, with two peaks of m/z 100 and 200, and intensity 1 and 2, respectively.
1000 2200 1
100 1
200 2
Note that the above is both an input and output format. If you wanted to make up a peak list, you could serialize your data in the above format and it'd be readable by the IO Framework and any tool that uses the IO Framework.
Applied Biosystems: .t2d, .bic, and .wiff
Applied Biosystems has a number of file formats including the T2D format used by their MALDI TOFTOF 4700 and 4800 instruments and the .bic file format used by the Voyager mass spectrometer.
- .t2d
- Complete support is provided for reading and writing files in the T2D format. The support is based on the ProteomeCommons.org IO-T2D project, which was created in collaboration with Applied Biosystems. Further documentation may be found in the "ProteomeCommons.org IO-T2D" project at ProteomeCommons.org
- .bic
- Voyager instruments produces a .bic file and a text file for a continuous spectrum. Support for reading and writing this format is currently being worked on.
- .wiff
-
Support exists for reading Analyst WIFF files from a QStar or QTrap 2000 or QTrap 4000 using the Analyst software libraries and the wiff2dta tool1. In order to use this functionality you must be using Microsoft Windows as your operating system and you must have installed ABI's Analyst and have a local copy of the wiff2dta program. Use the following steps to get everything installed.
- Install ABI's Analyst software package.
- Download a copy of the wiff2dta program from http://sourceforge.net/projects/protms/. This should be a direct link to the download page.
- When using the IO framework do one of the following
- Set the JVM parameter "
-Dwiff2data [wiff2dta.exe]
" replacing [wiff2dta.exe]
with wherever you put the copy of the program, e.g. "-Dwiff2data wiff2dta_1108_analyst141.exe
".
- Copy the wiff2dta program executable to your working directory, i.e. the directory you are executing Java from.
- Copy the wiff2dta program in to your classpath and name it "
wiff2dta.exe
"
References
Andreas M Boehm, Robert P Galvin, and Albert Sickmann, "Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing", BMC Bioinformatics 2004, 5:162 doi:10.1186/1471-2105-5-162
Thermo Finnigan .raw
Read support is available for Thermo Finnigan's RAW file format via the ReAdW package from the Sashimi project. You must have Thermo Finnigan's XCalibur DLL to use this functionality. Use the following steps to enable RAW file reading.
- Install Thermo Finnigan's XCalibur 2.0+
- Download a copy of the ReAdW program from http://sashimi.sf.net
- Add ReAdW.exe to
C:/Program Files/ProteomeCommons.org/IO/ReAdW.exe
. If you have ReAdW.exe installed elsewhere, the GUI will prompt you for its location.
Special Note: When using the ReAdW tool to read .raw files a mzXML file is generated by ReAdW then converted by the IO Framework in to the desired format. If you want mzXML and you want the exact mzXML that ReAdW produces, select the "Don't Convert" option.
ISB/PSI lead mzData and mzXML merge effort dataXML
Efforts lead by the ISB and PSI are underway to merge the mzXML and mzData file formats. The working name for the new file format is dataXML. Beta-support exists for this file format; however, currently very few tools use this format and certainly it'll change before the final version is released. You are not encouraged to use the beta dataXML format unless you simply want to see what it looks like.
Select the "dataXML (beta)" file format option to use dataXML file format. Both read and write support exists; however, full support for dataXML's meta-data is not exposed through the GUI.
mzXML
mzXML is an open, XML based file format designed by Systems Biology. The framework supports reading either peak list or spectral data that is in the mzXML file format support as described n the mzXML schema and documentation. This framework provides read support of peak lists and spectra in *.mzXML files. Proper stream-based XML parsing is used, allowing for mzXML files of any size to be used. Proper Base64 decoding is also used, allowing for data in either 32 bit or 64 bit precision.
mzXML support by version
- mzXML version 1.1.1
- Near complete read and write support is implemented for mzXML 1.1.1 with lack of complete support for spotting and separation information. Any document with the mzXML 1.1.1 schema declared will be automatically read. Alternatively, files ending in
.1.1.1.mzxml.xml
will automatically be treated as files in mzXML 1.1.1 format.
- mzXML version 2.0
- Near complete read and write support is implemented for mzXML 2.0 with lack of complete support for spotting and separation information. Any document with the mzXML 2.0 schema declared will be automatically read. Alternatively, files ending in
.2.0.mzxml.xml
will automatically be treated as files in mzXML 2.0 format.
- mzXML version 2.1
- Near complete read and write support is implemented for mzXML 2.1 with lack of complete support for spotting and separation information. Any document with the mzXML 2.1 schema declared will be automatically read. Alternatively, files ending in
.2.1.mzxml.xml
will automatically be treated as files in mzXML 2.1 format.
Helpful mzXML links.
Proteomics Standards Initiative (PSI) .mzData
mzData is an open, XML based file format designed by US HUPO. The framework supports reading and writing data that is in the mzData file format as defined by the schema and accompanying documentation. Proper stream-based XML parsing is used, allowing for mzData files of any size to be used. Proper Base64 decoding is also used, allowing for data in either big endian or little endian format and data in either 32 bit or 64 bit precision.
- mzData version 1.04
- Read support for mzData 1.04 is provided by the mzData 1.05 reader described below. Write support is currently not available for mzData 1.04.
- mzData version 1.05
- Read and write support exist for the mzData 1.05 format. Any document with the mzData 1.05 schema declared will be automatically read. Alternatively, files ending in
..mzdata
will automatically be treated as files in mzData 1.05 format.
Helpful mzData links.
National Institute of Standards and Technology (NIST) Library of Peptide Ion Fragmentation Spectra .msp
Steve Stein from the NIST has been working on creating high quality spectral libraries of MS/MS data. This data is available in several different formats along with a search tool. You can download the data from several locations including ProtoemeCommons.org. The primary format intended for other's use is a custom, simple, plain-text format that uses the '.msp' extension.
The IO framework includes read support for data in the .msp file format. Along with the standard MS/MS peak list information the file format also includes information about the peptide sequence that most likely matches each spectrum. If you are interested in accessing this peptide sequence information, you can sub-cast any PeakList object returned by the MSPPeakListReader class to MSPPeakList as illustrated below.
PeakListReader plr = GenericPeakListReader.getPeakListReader("C:/data/example.msp");
// get the abstract PeakList object -- no information about peptide sequence
PeakList pl = plr.getPeakList();
// sub-cast to get peptide sequence info, if desired.
MSPPeakList msppl = (MSPPeakList)pl;
msppl.getPeptides();
...
X!Tandem Output Files (aka TheGPM output) .xml, .thegpm.xml, .tandem.xml, .amethyst.xml, .opal.xml, .jasper.xml
The X!Tandem MS/MS search engine, which is used by TheGPM, produces output files that include both the identified peptide and protein sequences and the MS/MS peak lists that where identified. Several data sets, including Jasper, Amethyst, and Quartz, are published by the TheGPM.org in this format. The ProteomeCommons.org IO Framework can be used to read through X!Tandem output files and retreive the included peak lists. This is a convenient method of converting peak lists that X!Tandem identifies in to format that may be more familiar such as MGF or DTA.
Peptide and protein information associated with peak lists in X!Tandem output files are included in PeakList objects returned by the X!Tandem PeakListReader
implementation. If you wish to access associated peptide sequences, sub-cast the PeakList
object to a XTandemOutputPeakList
as illustrated below.
PeakListReader plr = GenericPeakListReader.getPeakListReader("C:/data/example.msp");
// get the abstract PeakList object -- no information about peptide sequence
PeakList pl = plr.getPeakList();
// sub-cast to get peptide sequence info, if desired.
XTandemOutputPeakList xtopl = (XTandemOutputPeakList)pl;
xtopl.getPeptides();
...
Auto-compression/decompression support
Support exists for seamlessly using several compression algorithms with peak list formats. These compression formats are not peak list formats themselves, rather formats that can compress existing peak list files. In cases of the very verbose XML formats such as mzData and mzXML the compression can save lots of space.
- ZIP
-
Complete read/write support exists for the ZIP format. Any file ending with .<extension>l;.zip
, e.g. example.mgf.zip
uses .mgf as the extension, will be read or serialized assuming use of the ZIP format.
The ZIP algorithm supports more than one file bundled together. The IO Framework will only read the first peak list included in a ZIP with multiple files. Note, the ZIP algorithm is possible the most widely supported algorithm, but it normally doesn't provide as good of compression as LZMA or bzip2.
Here are some helpful ZIP links
- GZIP
-
Complete read/write support exists for the GZIP format. Any file ending with .<extension>l;.gzip
or .<extension>l;.gz
, e.g. example.mgf.gz
uses .mgf as the extension, will be read or serialized assuming use of the GZIP format.
Here are some helpful GZIP links.
- bzip2
-
Complete read/write support exists for the BZIP2 format. Any file ending with .<extension>l;.bzip2
or .<extension>l;.gz
, e.g. example.mgf.gz
uses .mgf as the extension, will be read or serialized assuming use of the BZIP2 format.
Here are some helpful BZIP2 links.
- LZMA
-
Complete read/write support exists for the LZMA format. Any file ending with .<extension>l;.LZMA
or .<extension>l;.gz
, e.g. example.mgf.gz
uses .mgf as the extension, will be read or serialized assuming use of the LZMA format.
LZMA is generally the best compression algorithm available; however, the benefit is normally marginal (5-10%) compared to the other formats.
Here are some helpful LZMA links.
Frequently Asked Questions (FAQ)
This is a list of frequently asked questions based on user e-mails from the ProteomeCommons.org e-mail list.
What does the "Don't Convert" option do?
A few of the file formats supported by the IO Framework rely on other tools. Namely ReAdW for .raw files and CompassXport for Bruker files. In these cases the associated tool makes an mzXML file and the IO Framework converts that file to the desired final file format.
The "Don't Convert" option tells the IO Framework to leave the mzXML file alone. Instead of using the mzXML as an intermediate file a copy of it will be saved in the selected output directory.
What does the "Merge" option do?
The "Merge" option will concat all of the input files in to one single output file. Handy for squeezing many files in to a single .mgf for Mascot searches and the like.
How do I disable that annoying popup box, aka "Unhandled Win32 Exception" or "Windows Error Reporting"?
A popup box may appear whenever native Windows code throws an exception, which may happen when using native libraries such as ReAdW.exe to read data in the RAW file format. This popup box is Window's Just-In-Time debugger (JIT), and it mostly appears on machines that have installed Visual Studio. To disable this debugger, delete the following registry keys as specified by the MSDN documentation.
Disabling JIT-attach Debugging
After Visual Studio is installed on a server, the default behavior when an unhandled exception occurs is to show an Exception dialog that requires user intervention to either start Just-In-Time debugging or ignore the exception. This may be undesirable for unattended operation. To configure the server to no longer show a dialog when an unhandled exception occurs (the default behavior prior to installing Visual Studio), use the registry editor to delete the following registry keys:
- On 32 bit machines
- HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AeDebug\Debugger
- HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\.NETFramework\DbgManagedDebugger
- On 64 bit machines
- HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows NT\CurrentVersion\AeDebug\Debugger
- HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\.NETFramework\DbgManagedDebugger
If you are a developer, you'll probably want to enable the JIT when coding. To do this, follow the below instructions from MSDN.
Enabling JIT-attach Debugging
JIT-attach debugging is the phrase used to describe attaching a debugger to an executable image that throws an uncaught exception. In unmanaged code, it is what happens when you see a message box that invites you to:
- Click OK to terminate the program
- Click CANCEL to debug the program
If you click CANCEL, a debugger is started and attached to the process. The registry key that controls this is called HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\Current Version\AeDebug
.
For an application that includes managed code, the common language runtime will present a similar dialog to JIT-attach a debugger. The registry key that controls this option is called HKEY_LOCAL_MACHINE\Software\Microsoft\.NETFramework\DbgJITDebugLaunchSetting
.
- If value = 0, prompt the user by means of a message box. This only applies to processes that are interactive with the desktop; services and other noninteractive processes will terminate.
In the .NET Framework versions 1.0 and 1.1, or the .NET Framework version 2.0 on Windows 98 and Windows Me, the message box choices are:
- Continue. This results in a stack dump to the console and process termination.
- Attach a debugger. In this case, the runtime spawns the debugger listed in the DbgManagedDebugger registry key. If none is found, the process is terminated.
- In the .NET Framework version 2.0 on platforms other than Windows 98 and Windows Me, the choices are:
- Send. An error report is sent to Microsoft, followed by process termination. See http://winqual.microsoft.com for information on how to retrieve these reports.
- Don't Send. This results in a stack dump to the console and process termination.
- Debug. The runtime spawns the debugger listed in the DbgManagedDebugger registry key. If none is found, the process is terminated.
- If value = 1, simply return control. This results in a stack dump, after which the process is terminated.
- If value = 2, spawn the debugger listed in the DbgManagedDebugger registry key.
- If value = 16, in the .NET Framework version 2.0 only, the runtime presents the message box described above for processes that are interactive with the desktop. For processes that are not interactive, the runtime spawns the debugger listed in the DbgManagedDebugger registry key. This is the default setting for the .NET Framework version 2.0.
Finally, if you are doing batch processing of peak lists and you don't want it to be interrupted at all, you can also disable Windows XP error reporting. Follow the instructions described on MSDN also summarized below.
How to Configure and Use Error Reporting
You can enable, disable, or modify the way that error reporting works on a Windows XP-based computer. When an error occurs, a dialog box is displayed that prompts you to report the problem to Microsoft. If you want to report the problem, technical information about the problem is sent to Microsoft over the Internet. You must be connected to the Internet to use the feature. If a similar problem has been reported by other users and information about the problem is available, you receive a link to a Web page that contains information about the problem.
To access the settings for the reporting feature:
- Click Start.
- Right-click My Computer, then click Properties.
- Click the Advanced tab.
- Click Error Reporting.
To configure the error reporting feature:
- By default, error reporting is enabled. To disable it, click Disable error reporting. To continue to be notified when errors occur without being prompted to report the errors, click to select the But notify me when critical errors occur check box.
- Specify whether you want to use error reporting for the Windows operating system, for programs, or for both Windows and programs.
- To report errors only for selected programs, click Choose Programs, click All programs in this list, and then click the programs that you do not want to include.
- To add a program that is not listed, click Add, type the name of the program, or click Browse to find the program on your computer.
- If many programs are listed, you may want to create an exclude list. In the Do not report errors for these programs box, click Add, type the name of each program that you want to exclude from error reporting, or click Browse to find the program on your computer.
Where is that peak list conversion tool?
The on-line GUI tool that converts peak lists is here.
Why doesn't "java -jar ProteomeCommons.org-IO.jar
" work?
The JAR file included with the code is not executable. It is intended to be used as a Java library, i.e. "java -cp ProteomeCommons.org-IO.jar ". If you'd like to run the example programs from command line, try executing "java -cp ProteomeCommons.org-IO.jar org.proteomecommons.io.util.PrintPeakList peaklist file
", where you replace peaklist-file with the location of a real peak list.
Where do I get help?
Generally speaking, this is free, open-source code. You don't get free tech support with your download. However, there are options for getting help. The best help comes straight from the people who made this code. If you are willing to hire the core developers to help with your problem or to teach you how the framework works, contact Jayson Falkner. If you want free help, use the e-mail list at ProteomeCommons.org. Most of the developer and users of this framework are on that e-mail list, and it is the appropriate place to look for free advice.
Links
This is a list of links that references other projects that can read/write various mass spectrometry file formats. In most cases these are commercial tools that are either bundled with mass spectrometers or that cost a significant amount of money. If you know of a tool that isn't on this list, please send in the information to this project's developers.
- Sashimi Project
- The Institute for Systems Biology (ISB) started and has maintained a great collection of tools for reading and converting to the mzXML file format. Support exists for most of the popular file formats, particularly .raw; however, most of the software does require users to have vendor-specific binaries available.
- CompassXport
- Bruker's CompassXport utility is a great, unofficially-supported tool from Bruker for reading the common data files generated by Bruker instruments. The tool dumps data in to mzXML format and it may be used in a batch mode. You must be registered and logged in to Bruker's website in order to download the CompassXport tool. Helpful instructions for doing so are provide by both IonSource and Bioinformatics Solutions Inc.
- wiff2dta
- The wiff2dta program is designed to use the ABI Analyst binaries to efficiently export MS and MSMS data to a number of formats including mzXml and MGF. The program can run in either a interactive GUI mode or a batch mode.
- CCWiffer
- CCWiffer is a software package designed to converting WIFF data files to the mzXML and mzData formats. Although, as of the PSI 2006 meeting it appeared to not successfully create either format.
- PyMsXML
- PyMsXML is a python script for converting vendor specific mass spectrometry data files for Applied Biosystems' Q-Star, 4700, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML, from the Sashimi Glossolalia project of the Institute for Systems Biology (ISB); and mzData, from the Proteome Standards Initiative (PSI) project of the Human Proteome Organization (HUPO).
- Applied Biosystems WIFF to mzData
- A WIFF to mzData translator from ABI.
- ProteinScape
- Bruker Daltonics proteomics platform.
- BioWorks 3.2
- BioWorks is Thermo Finnigan's proteomics platform and it can export in mzData format.
- Kratos Launchpad
- We couldn't find proper documentation; however, this should be the tool for working with Shimadzu data and generating mzData documents.
- Waters ProteinLynx Global SERVER
- Waters bioinformatics platform. It has many features including the ability to input and output data in mzData format.
- Mascot Distiller
- "Mascot Distiller Workstation offers a single, intuitive interface to a wide range of native (binary) mass spectrometry data files. A unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists. This core functionality can be extended by adding one or more toolboxes. These are optional collections of tools for specific tasks, such as Mascot search result review, automatic and manual de novo sequencing, and batch processing. There is also a developer's package that provides access to the API of the underlying COM library."
- MZmime
- "MZmine is a platform-independent software for data processing needed in differential analysis of LC/MS data, with applications in metabolomics and proteomics. The software is expandable to other types of data such as GC/MS and CE/MS. Our aim and motivation have been to develop a modular and vendor independent software package that enables easy integration of new algorithms and applications into the data processing pipeline."
- The Proteios Project
- A project designed to organize and share proteomics data. It can export in mzData format.
- BioJava Project
- A Java project designed to provide a general set of tools for Bioinformatics developers including code that can read and manipulate protein sequences in FASTA files. No mass spectrometer file formats are supported.
Todo List
This is the list of features that need to be done. If you are interested in helping out, please get in touch.
- Preserve MGF meta-data in concatinated peak lists. Currently MGF meta-data (specifically TITLE attributes) are being lost when peak lists are converted. Fix the MascotGenericFormatWriter to properly preserve this information.
- Fix DTA conversion. If a parent mass isn't know Integer.MIN_VALUE is used.
Licensing Information
The goal of this project is to provide free, open-source code that anyone may use as they please; However, everyting in this project is strictly licensed under the Apache 2.0 license. This protects the authors and contributors of this project, and it encourages fair use of the code. A copy of the Apache 2.0 license may be found on-line at http://www.apache.org/licenses/LICENSE-2.0 or as plain text in the LICENSE.txt file included in this archive.
In addition to the Apache 2.0 license it is requested that any person or organization that uses the ProteomeCommons.org IO Framework properly reference this project. In at least one public, appropriate place, please note that the "ProteomeCommons.org IO Framework" is being used, and provide a URL to http://www.proteomecommons.org/current/531.
If you have further questions or comments regarding this project, please contact Jayson Falkner


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WITNESS LIST
Insurance Committee
April 16, 2019 - 8:00 AM
Registering, but not testifying:
For:
MacDougal, Vanessa (Self)
Simpson, Matt (ACLU of Texas)
Spreen, Lauren (Texas Academy of Family Physicians)
Stewart, Clayton (Texas Medical Association)
Webb, Dale (Self)
Wendell, Ware (Texas Watch)
Wittenburg, Michelle (Self; Kk125 ovarian cancer research foundation)
Against:
Boston, Jessica (Texas Association of Business)
Dudensing, Jamie (Texas Association of Health Plans)
On:
Bewer, Pat (Texas Department of Insurance)
Bowden, Rachel (Texas Department of Insurance)
For:
Hansch, Greg (National Alliance on Mental Illness (NAMI) Texas)
Registering, but not testifying:
For:
Allen, Philip (Self; Texas Counselors Association)
Alvarado, Melissa (Self)
Anthony-Benavides, Erica (Self; Escalada Education Co.)
Bell, Jeane (Self)
Bullard, Becky (Self)
Bunker, Phil (Self)
Caceres, Susan (Self)
Cheng, Ashley (Self)
Cogan, Alex (Self)
DeVoll, Michael (Self)
Dower, Carolyn (Self)
Doyle, Cynthia (Self)
Dunkelberg, Anne (Center for Public Policy Priorities)
Francis, Will (National Association of Social Workers - Texas Chapter)
Friese, Jan (Texas Counseling Associatio)
Gardiner, Carley (Self)
Gidseg, Joey (Self; Texas Democrats with Disabilities)
Gilpin, Brittany (Self)
Guy, Linda (Self)
1
WITNESS LIST
For:
Hartman, Marilyn (Self; NAMI Austin)
Hughes, Lisa (Texas Academy of Nutrition and Dietetics)
Irwin, Shellie (Self; TCA)
Keller, Merily (Self; Texas Suicide Prevention Council)
MacDougal, Vanessa (Self)
Ramberg, Frances (Self)
Reardon, Sarah (Self)
Saxton, Josette (Texans Care for Children)
Simon, Arthur (Self)
Smith, Bernadette (Self; Texas counseling association)
Stewart, Kevin (Texas Psychological Association)
Sughrue, Alissa (National Alliance on Mental Illness (NAMI) Texas)
Triebel, Joanna (Self)
Vunderink, Gregg (Self)
Webb, Dale (Self)
Yanas, Christine (Methodist Healthcare Ministries of South Texas , Inc.)
Against:
Boston, Jessica (Texas Association of Business)
Dudensing, Jamie (Texas Association of Health Plans)
Spilman, Annie (NFIB)
On:
Bewer, Pat (Texas Department of Insurance)
Bowden, Rachel (Texas Department of Insurance)
Danzeiser, Doug (Texas Department of Insurance)
For:
Johnson-Patagoc, Kate (Self; Texas Associatin for Behavior Analysis Public Policy Group)
Registering, but not testifying:
For:
Benestante, Jacquie (Autism Society of Texas)
Broughal, Christine (Texans for Special Education Reform)
Dunkelberg, Anne (Center for Public Policy Priorities)
Francis, Will (National Association of Social Workers - Texas Chapter)
Hansch, Greg (National Alliance on Mental Illness (NAMI) Texas)
Hartman, Marilyn (Self; NAMI Austin)
Hoppe, Christina (Children's hospital association of Texas (CHAT))
Johnson, Lee (Texas Council of Community Centers)
Litzinger, Linda (Self; Texas Parent to Parent)
Masey, Chris (Coalition of Texans with Disabilities)
Meroney, Shannon (Texas Association of Health Underwriters (TAHU))
Rangel, Lauren (Easterseals central texas)
Sauceda, Nataly (United Ways of Texas)
2
WITNESS LIST
For:
Spreen, Lauren (Texas Academy of Family Physicians)
Stewart, Clayton (Texas Medical Association)
Travis, Clayton (Texas Pediatric Society)
Against:
Boston, Jessica (Texas Association of Business)
Dudensing, Jamie (Texas Association of Health Plans)
Spilman, Annie (NFIB)
On:
Bowden, Rachel (Texas Department of Insurance)
For:
Eiland, Craig (Self)
Registering, but not testifying:
For:
Wendell, Ware (Texas Watch)
Against:
Garcia, Joe (AmRisc, LLC)
Marlow, John (Chubb)
Martin, Paul (National Association of Mutual Insurance Companies)
Woods, Joe (American Property Casualty Insurance Association)
On:
Baker, Marianne (Texas Department of Insurance)
Essary, Norma (Surplus Lines Stamping Office of Texas)
For:
Cawley, Jennifer (Texas Association of Life and Health Insurers)
Registering, but not testifying:
For:
Dudensing, Jamie (Texas Association of Health Plans)
Meroney, Shannon (Texas Association of Health Underwriters (TAHU))
On:
Bowden, Rachel (Texas Department of Insurance)
Registering, but not testifying:
On:
Danzeiser, Doug (Texas Department of Insurance)
3
WITNESS LIST
On:
Dudensing, Jamie (Texas Association of Health Plans)
Registering, but not testifying:
For:
Anthony-Benavides, Erica (Self; Escalada Education Co.)
Bearden, Chase (Coalition of Texans with Disabilities)
Borel, Dennis (Coalition of Texans with Disabilities)
Bruce, Bonnie (Texas Society of Anesthesiologists)
Duncan, Cameron (Texas Hospital Association)
Francis, Will (National Association of Social Workers - Texas Chapter)
Gidseg, Joey (Self; Texas Democrats with Disabilities)
Guy, Linda (Self)
Hansch, Greg (National Alliance on Mental Illness (NAMI) Texas)
Hartman, Marilyn (Self; NAMI Austin)
Hutson, Blake (AARP Texas)
Masey, Chris (Coalition of Texans with Disabilities)
Ozuna, Jesse (Doctor's Hospital at Renaissance (DHR Health))
Pogue, Stacey (Center for Public Policy Priorities)
Rangel, Lauren (Easterseals Central Texas)
Sauceda, Nataly (United Ways of Texas)
Simon, Arthur (Self)
Spreen, Lauren (Texas Academy of Family Physicians)
Stewart, Clayton (Texas Medical Association)
Sughrue, Alissa (National Alliance on Mental Illness (NAMI) Texas)
Walker, Nancy (Texas Occupational Therapy Association)
Yanas, Christine (Methodist Healthcare Ministries of South Texas , Inc.)
Against:
Meroney, Shannon (Texas Association of Health Underwriters (TAHU))
On:
Bowden, Rachel (Texas Department of Insurance)
For:
McCraw, John (Self; Texas Trial Lawyers Association)
Wendell, Ware (Texas Watch)
Against:
Floyd, Beaman (Texas Coalition for Affordable Insurance Solutions)
Martin, Paul (National Association of Mutual Insurance Companies)
Thompson, Jay (Afact)
Woods, Joe (American Property Casualty Insurance Association)
4
WITNESS LIST
Registering, but not testifying:
On:
Baker, Marianne (Texas Department of Insurance)
For:
Overstreet, Morris (Self)
On:
Thompson, Jay (Talhi)
Registering, but not testifying:
For:
Allen, Elwynn (Self; Texas funeral director assoc)
Carnley, Zachary (Self)
Hilderbran, Harvey (Texas Funeral Directors Association (TFDA))
Lucas, Jimmy (Self; Texas Funeral Directors Association)
On:
Cawley, Jennifer (Texas Association of Life and Health Insurers)
Danzeiser, Doug (Texas Department of Insurance)
For:
Hill, Karen (Community Health Choice)
Pogue, Stacey (Center for Public Policy Priorities)
Against:
Meroney, Shannon (Texas Association of Health Underwriters (TAHU))
Registering, but not testifying:
For:
Bacon, Dana (The Leukemia & Lymphoma Society)
Bearden, Chase (Coalition of Texans with Disabilities)
Borel, Dennis (Coalition of Texans with Disabilities)
Chepkauskas, Daniel (Patient Choice Coalition of Texas)
Duncan, Cameron (Texas Hospital Association)
Francis, Will (National Association of Social Workers - Texas Chapter)
Hansch, Greg (National Alliance on Mental Illness (NAMI) Texas)
Hartman, Marilyn (Self; NAMI Austin)
Hench, Marina (American Cancer Society Cancer Action Network)
Hutson, Blake (AARP Texas)
Kuykendall (pronounced: KER-KIN-DOLL), Deanna L. (Texas Brain Injury Providers
Alliance)
Massey, Shelby (American Heart Association)
Nichols-Segers, Simone (National MS Society)
Ozuna, Jesse (Doctor's Hospital at Renaissance (DHR Health))
5
WITNESS LIST
For:
Patterson, TJ (City of Fort Worth)
Romo, Joel (American Diabetes Association)
Schauer, Tim (Community Health Choice)
Spreen, Lauren (Texas Academy of Family Physicians)
Stewart, Clayton (Texas Medical Association)
Sughrue, Alissa (National Alliance on Mental Illness (NAMI) Texas)
Yanas, Christine (Methodist Healthcare Ministries of South Texas , Inc.)
On:
Danzeiser, Doug (Texas Department of Insurance)
For:
Shields, Bradford (Texas Academy of Audiology)
Registering, but not testifying:
For:
Masey, Chris (Coalition of Texans with Disabilities)
Rangel, Lauren (Easterseals Central Texas)
Stewart, Clayton (Texas Medical Association)
Against:
Boston, Jessica (Texas Association of Business)
Dudensing, Jamie (Texas Association of Health Plans)
Spilman, Annie (NFIB)
On:
Bewer, Pat (Texas Department of Insurance)
Bowden, Rachel (Texas Department of Insurance)
Dudensing, Jamie (Texas Association of Health Plans)
For:
Floyd, Beaman (Texas Coalition for Affordable Insurance Solutions)
Thompson, Jay (Afact)
Thompson, Jay (Nicb)
Registering, but not testifying:
For:
Martin, Paul (National Association of Mutual Insurance Companies)
Ostrander, Rita (Combined Law Enforcement Associations of Texas)
Woods, Joe (American Property Casualty Insurance Association)
On:
Davis, Chris (Texas Department of Insurance)
Johnson, Kyson (Texas Department of Insurance)
6
WITNESS LIST
For:
Bordelon, Rod (Texans for Free Enterprise)
Day, Aaron (Texas Land Title Association)
Registering, but not testifying:
For:
Fuentes, Frank (Self; U.S. Hispanic Contractors Association)
Hoy, Sandy (Texas Apartment Association)
Keener, Justin (Self; Texans for Free Enterprise, Americans for Prosperity, Doug Deason, Libre
Initiative, Concerned Veterans for America)
Lee, Randy (Stewart Title Guaranty Company and First American Title Insurance Company)
Against:
Del bosque, Nora (Titledata Inc)
On:
Baker, Marianne (Texas Department of Insurance)
For:
Flores, John (Self; Texas Medical Association)
Against:
Dudensing, Jamie (Texas Association of Health Plans)
Registering, but not testifying:
For:
Bruce, Bonnie (Texas Society of Anesthesiologists)
Chepkauskas, Daniel (Patient Choice Coalition of Texas)
Guy, Linda (Self)
Lucas, Tommy (Self; Texas Optometric Association)
Masey, Chris (Coalition of Texans with Disabilities)
Spreen, Lauren (Texas Academy of Family Physicians)
Against:
Boston, Jessica (Texas Association of Business)
Kelly, Bill (Mayor’s Office, City of Houston)
For:
Buck, James (Texas Legal)
Thompson, Jay (Texas legal protection plan)
Registering, but not testifying:
On:
Danzeiser, Doug (Texas Department of Insurance)
7
WITNESS LIST
For:
Lopez, Frederick (Self; The Center fo Neurology and Neurophysiology, PA)
Registering, but not testifying:
For:
Bruce, Bonnie (Texas Society of Anesthesiologists)
Duncan, Cameron (Texas Hospital Association)
Lucas, Tommy (Self; Texas Optometric Association)
Against:
Dudensing, Jamie (Texas Association of Health Plans)
On:
Bewer, Pat (Texas Department of Insurance)
Bowden, Rachel (Texas Department of Insurance)
Registering, but not testifying:
On:
Mellott, Shelly (Texas Department of Motor Vehicles)
Worman, Mark (Texas Department of Insurance)
For:
Brougham, Nancy (Self)
Cronin, Bill (Dignitana, Inc.)
DeJean, LaShaune (PAXMAN US)
Koller, Sarah (Self)
Nangia, Julie (Self)
Registering, but not testifying:
For:
Stewart, Clayton (Texas Medical Association)
Wendell, Ware (Texas Watch)
Against:
Boston, Jessica (Texas Association of Business)
Dudensing, Jamie (Texas Association of Health Plans)
Spilman, Annie (NFIB)
On:
Bewer, Pat (Texas Department of Insurance)
Bowden, Rachel (Texas Department of Insurance)
Against:
Floyd, Beaman (Texas Coalition for Affordable Insurance Solutions)
8
WITNESS LIST
Against:
Martin, Paul (National Association of Mutual Insurance Companies)
Woods, Joe (American Property Casualty Insurance Association)
Registering, but not testifying:
For:
Bakko, Sally (City of Galveston)
Brannan, Ryan (Coastal Windstorm Insurance Coalition)
Thompson, Jay (Afact)
Against:
Marlow, John (Chubb)
On:
Polak, John (TWIA)
Ryder, Brian (Texas Department of Insurance)
For:
Balat, David (Texas Public Policy Foundation)
Lindley, Katarina (Self; DPCAction)
Registering, but not testifying:
For:
Spreen, Lauren (Texas Academy of Family Physicians)
Stewart, Clayton (Texas Medical Association)
Against:
Lara, Rene (Texas AFL-CIO)
Sheldon, Tyler (Texas State Employees Union)
On:
Bowden, Rachel (Texas Department of Insurance)
Danzeiser, Doug (Texas Department of Insurance)
For:
Floyd, Beaman (Texas Coalition for Affordable Insurance Solutions)
Loftis, Lee (Independent Insurance Agents of Texas)
Thompson, Jay (Afact)
Against:
Arizpe, Marco (Self)
Berryman, Frank (Self)
Brooks, Joseph (Self; Complete Curb Products)
Castillo, Carlos (Self; Casa engineering)
Daily, Terrill (Self)
Day, David (Self)
Escamilla, Arnulfo (Self)
9
WITNESS LIST
Against:
Garcia, Juan (Self)
Hernandez, Daniel (Self; CASA Engineering, LLC)
Medrano jr, Francisco (Self; CASA engineering llc)
Richa, Eduardo (Self)
Registering, but not testifying:
For:
Boston, Jessica (Texas Association of Business)
Brannan, Ryan (Coastal Windstorm Insurance Coalition)
DeWitt, Cathy (USAA)
Finley, Trace (United Corpus Christi Chamber of Commerce)
Martin, Paul (National Association of Mutual Insurance Companies)
Woods, Joe (American Property Casualty Insurance Association)
Against:
Simon, Arthur (Self)
Voss, Ronald (Self)
On:
Nash, Carissa (Sunset Advisory Commission)
Polak, John (TWIA)
Ret, Elisabeth (Texas Department of Insurance)
10


cut by column
Useful to cut in text
EX, cut the IP address from
64 bytes from <IP_ADDRESS>: icmp_req=1 ttl=255 time=4.86 ms
cut -d " " -f4 -d is delimiter
-f is field


The Data Transfer Project allows you to securely transfer your data from one participating cloud service to another.
Before you start, you will need to have an account at both service providers. During the transfer process, you will be prompted to authenticate with each provider, so make sure you have your login information handy.


Free mediation
Mary Richards is willing to take part in telephone mediation.
You can try to resolve this dispute before a hearing with a mediator.
A mediator will:
- listen to each side separately - you won’t talk to directly to the other side
- ask you to consider what the other side says, but won’t make you compromise
- help you reach an agreement, if possible
More about how mediation works
Will you try mediation?
*Source: Money Claim Mediation Service statistics, April 2015 to March 2016.


本书pdf是 文字版 ，彩图版 。
Introduction
Laboratory Safety
Equipping a Home Chemistry Lab
Chemicals for the Home Chemistry Lab
Mastering Laboratory Skills
Laboratory: Separating Mixtures
Laboratory: Solubility and Solutions
Laboratory: Colligative Properties of Solutions
Laboratory: Introduction to Chemical Reactions and Stoichiometry
Laboratory: Reduction-Oxidation (Redox) Reactions
Laboratory: Acid-Base Chemistry
Laboratory: Chemical Kinetics
Laboratory: Chemical Equilibrium and Le Chatelier’s Principle
Laboratory: Gas Chemistry
Laboratory: Thermochemistry and Calorimetry
Laboratory: Electrochemistry
Laboratory: Photochemistry
Laboratory: Colloids and Suspensions
Laboratory: Qualitative Analysis
Laboratory: Quantitative Analysis
Laboratory: Synthesis of Useful Compounds
Laboratory: Forensic Chemistry


Sprinkled among the lakes and bayous in this northwestern part of the state are scenic state parks,
excellent fishing and hunting grounds, and great nature-viewing areas,
including portions of the Kisatchie National Forest, which spreads across some 600,000 acres.
Situated along the Red River, Shreveport is a popular destination in Louisiana. There are plenty of outdoor attractions for those who like to have fun outside, such as spending time at the zoo or parks. The Louisiana Boardwalk Outlets is a hub for outlet shopping, dining and recreation. For those who prefer to be indoors, there is even more to do, from museums and art galleries to aquariums and historic homes.