The open source project BALL consists of the versatile C++ class framework BALL (Biochemical Algorithms Library), a library of algorithms and data structures targeting molecular modelling and computational structural bioinformatics, a Python interface to this library and the open source graphical interface to BALL, the molecular viewer BALLView (also open source).

The library BALL is supplemented with a Python interface for scripting functionality. In addition, BALL offers command line utilities.

BALL has been ported to the operating systems Linux, Solaris, Microsoft Windows and MacOS X. BALL uses Qt as well as OpenGL. BALL has evolved from a commercial product into a free-of-charge, open source software licensed under the GNU Lesser General Public License (LGPL).

Its molecular viewer BALLView is developed by the ball project team as well and allows for the three dimensional visualization as well as direct application of the algorithms of the BALL library via it's graphical user interface.

BALLView uses OpenGL and the real time ray tracer RTFact as render backends. For both BALLView offers stereoscopic visualization in several different modes.

BALLView is a C++ application of BALL and is available under the GPL license for Linux, Solaris, Microsoft Windows, and MacOS X.

The BALL project is developed and maintained by groups at Saarland University, Mainz University, and University of Tübingen. Both the library and the viewer are heavily used for education and research alike. BALL packages have been made available in the Debian project in 04/2010.

Key features

Interactive molecular drawing and conformational editing (+)

Reading and writing of molecular file formats (PDB, MOL2, MOL, HIN, XYZ, KCF, SD, AC)

Reading secondary data sources e.g. (DCD, DSN6, GAMESS, JCAMP, SCWRL, TRR)

Generating molecules from and matching of SMILES- and SMARTS expressions to molecules

Geometry optimization

Minimizer and molecular dynamics classes

Support for force fields (MMFF94, AMBER, CHARMM) for scoring and energy minimization

Python Interface and scripting functionality

Plugin infrastructure (3D Space-Navigator, WII-based head tracking*, OpenSim*)

Molecular graphics (3D, stereoscopic viewing, ray tracing*)(+)

comprehensive documentation (Wiki, code snipets, online class documentation, bug tracker)

comprehensive regression tests

BALL project format for presentations and collaborative data exchange (+)

QSAR*

NMR

editable shortcuts (+)

(*) Experimental functionality of the next version

(+) functionality of BALLView

BALL library

The Biochemical Algorithms Library BALL is a comprehensive rapid application development framework for structural bioinformatics. BALL has been carefully designed to address programming experts as well as novices. Users can take advantage of BALL's rich functionality while being offered an extensive framework of C++ data structures and algorithms. A variety of standard structural bioinformatics algorithms are offered and new algorithms can be easily added.

Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers.

;File Import/Export: BALL supports a rich variety of molecular file formats like PDB, MOL2, MOL, HIN, XYZ, KCF, SD, AC as well as secondary data sources like DCD, DSN6, GAMESS, JCAMP, SCWRL, and TRR. Molecules can also be created using BALL’s peptide builder or based on SMILES expressions.

;General Structure Analysis: Further preparation and structure validation is enabled by, e.g., Kekuliser-, Aromaticity-, Bondorder-, HBond-, and Secondary Structure processors. A Fragment Library automatically infers missing information, e.g., a protein’s hydrogens or bonds. A Rotamer Library allows determining, assigning, and switching between a protein’s most likely side chain conformations. BALL’s Transformation processors guide generation of valid 3D structures. Its selection mechanism enables to specify parts of a molecule by simple expressions (SMILES, SMARTS, element types). This selection can be used by all modeling classes like the processors or force fields.

;Molecular Mechanics: Fast and stable implementations of the popular force fields CHARMM, Amber, and MMFF94 can be combined with BALL’s minimizer and simulation classes (steepest decent, conjugate gradient, L-BFGS, and shifted L-VMM).

A variety of standard structural bioinformatics algorithms are offered and new algorithms can be easily added.

Example

The following program reads a PDB file, adds missing information like bonds and hydrogens, optimizes the hydrogen positions using the AMBER force field, and writes the resulting molecule into a second pdb file.

using namespace std; using namespace BALL;

int main() { // read a PDB file PDBFile file("test.pdb"); System S; file >> S; file.close();

// add missing information // e.g. hydrogens and bonds FragmentDB fragment_db(""); S.apply(fragment_db.normalize_names); S.apply(fragment_db.add_hydrogens); S.apply(fragment_db.build_bonds);

// check for charges, bond lengths, // and missing atoms ResidueChecker checker(fragment_db); S.apply(checker);

// create an AMBER force field AmberFF FF; S.deselect(); FF.setup(S); Selector selector("element(H)"); S.apply(selector);

// optimize the hydrogen's positions ConjugateGradientMinimizer minimizer; minimizer.setup(FF); minimizer.setEnergyOutputFrequency(1); minimizer.minimize(50);

// write a PDB File file.open("test_out.pdb", ios::out); file << S; file.close(); }

Python Interface

SIP is used to automatically create python classes for all relevant C++ classes in the BALL library to allow for the same class interfaces. The Python classes have the same name as the C++ classes, so porting code that uses BALL from C++ to Python (and vice versa) is usually a trivial task.

For instance, the above C++ code translates to

# Example file = PDBFile("test.pdb") system = System() file.read(system) file.close()

# add missing information # e.g. hydrogens and bonds fragment_db = FragmentDB("") system.apply(fragment_db.normalize_names) system.apply(fragment_db.add_hydrogens) system.apply(fragment_db.build_bonds)

# check for charges, bond lengths, # and missing atoms checker = ResidueChecker(fragment_db) system.apply(checker)

# create an AMBER force field FF = AmberFF() system.deselect() FF.setup(system) selector = Selector("element(H)") system.apply(selector)

# optimize the hydrogen's positions minimizer = ConjugateGradientMinimizer() minimizer.setup(FF) minimizer.setEnergyOutputFrequency(1) minimizer.minimize(50)

# write a PDB File outfile = PDBFile("test_out.pdb", File.MODE_OUT) outfile.write(system) outfile.close()

The python interface is fully integrated into the viewer application BALLView and thus allows for direct visualization of results computed by python scripts. In addition, BALLView can be operated from the scripting interface and recurring tasks can be automated.

BALLView

BALLView is BALL’s standalone molecular modeling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.

BALLView offers standard visualization models for atoms, bonds, and surfaces as well as grid based visualization for e.g. electrostatic potentials. BALLView allows to load a number of molecules at the same time and all representations can be hidden or shown at will. A large part of the functionality of the library BALL can be applied directly to the loaded molecule in BALLView.

BALLView supports a number of modern visualization and input methods like, e.g., different stereo modes, space navigator, and VRPN-supported Input devices.

At CEBIT 2009, for BALLView was prominently presented as the first complete integration of real-time ray tracing technology into a molecular viewer and modelling tool.

See also

List of molecular graphics systems

List of software for molecular mechanics modeling

Molecular graphics

References

Further reading

External links

BALL project web page

BALLView web page

Code Library

Gallery

Tutorials

Category:C++ libraries Category:Computational chemistry software Category:Molecular modelling software Category:Bioinformatics software Category:Free bioinformatics software

de:BALL it:BALL pl:BALLView

name	Cheyenne Jackson
birth date	July 12, 1975
birth place	Newport, Washington, U.S.
occupation	Actor/Singer
years active	2002–present
spouse	Monte Lapka (since 2011)
partner	Monte Lapka (since 2000)
website	CheyenneJackson.com }}

Cheyenne Jackson (born July 12, 1975) is an American actor and singer. He started in regional theater when he moved to Seattle, and after moving to New York City, made his 2002 Broadway theatre debut understudying both male leads in the Tony Award-winning musical ''Thoroughly Modern Millie''. In 2005, he originated his first Broadway leading role in ''All Shook Up'' earning him a Theatre World Award for "Outstanding Broadway Debut".

In films, Jackson portrayed 9/11 victim and hero Mark Bingham in the 2006 Academy Award nominated ''United 93'' which earned him the Boston Society of Film Critics 2006 award for "Best Ensemble Cast". He has also appeared in the films ''Curiosity'' (2005), ''Hysteria'' (2010), ''The Green'' (opposite Julia Ormond and Illeana Douglas), and ''Price Check'' (with Parker Posey). On television, he is a recurring series regular on NBC's ''30 Rock'', portraying Danny Baker, and on Fox's ''Glee'' as Vocal Adrenaline coach Dustin Goolsby. He has also guest starred on several series including ''Curb Your Enthusiasm'', ''Lipstick Jungle'', ''Life on Mars'', ''Law & Order'', and ''Ugly Betty''. In 2008, Jackson played series lead Sebastian Kinglare for the Lifetime Television pilot ''Family Practice'' opposite Anne Archer and Beau Bridges. The series was not picked up for distribution.

Jackson has starred in several notable webisode series and in 2009 starred in a sold out one man show, "Back to the Start." In 2008, he was named ''Out'' magazine's Entertainer of the Year. He is an international ambassador for amfAR (The Foundation for AIDS Research) and a national ambassador and spokesperson for The Hetrick-Martin Institute.

Early life

Jackson was born in Idaho on July 12, 1975, and was named by his father after the 1950s Western series. The third of four children, he was raised in Newport, Washington, a "teeny mill town" of about 1,200 people in a rural area on the Washington-Idaho border. His father is a Native American and a Vietnam veteran.

His mother taught Jackson, his sister and two brothers to sing and regularly played music from Joan Baez, Joni Mitchell, Bob Dylan and Elvis. He moved to Spokane, Washington as a teenager and came out to his parents as gay at age 19. His parents were evangelical born-again Christians and his brother is a pastor who has preached on ''The 700 Club''. They eventually accepted his sexuality.

In Seattle, he worked as an ad executive at a magazine and did some theater on the side, earning his Equity card. "As soon as I found out what theater was, what Broadway was, I thought, ''Oh, that's what I'll do with my life.'' Just a matter of getting all the pieces in place." Inspired to rethink his career after both a death in his family and the September 11 attacks, he moved to New York.

Career

Early in his career, Jackson worked as a back-up singer for Vanessa Williams, Heather Headley, and Liza Minnelli. In regional theaters, Jackson has appeared as Tony in ''West Side Story'', as Joey in ''The Most Happy Fella'', as Cain in ''Children of Eden'', as Berger in ''Hair'', as Billy Bigelow in ''Carousel'', as Joe Hardy in ''Damn Yankees'', as Rocky in ''The Rocky Horror Show'', and as The Poet in ''Kismet'', among many other productions.

Jackson made his Broadway debut understudying both male leads in the Tony Award-winning musical ''Thoroughly Modern Millie''. He later served as the standby for the character of Radames in ''Aida'', then originated the role of Matthew in the off-Broadway production of ''Altar Boyz''. In 2005, he originated his first Broadway leading role in the musical ''All Shook Up'', a tribute to Elvis Presley. His performance as Chad earned him much critical praise, the Theatre World Award, and nominations from the Drama League and Outer Critics Circle Awards for Outstanding Lead Actor. In 2006, he starred off-Broadway in playwright Nicky Silver's ''The Agony and The Agony'' with Victoria Clark. In June 2007, less than a week before the scheduled opening night, Jackson assumed the lead role of Sonny on Broadway in ''Xanadu'', replacing James Carpinello who had been injured during rehearsal. Previous workshop productions of the musical starred Jackson and Jane Krakowski. However, both Jackson and Krakowski opted out of the initial Broadway run, citing schedule conflicts. His performance as Sonny earned him nominations from the Drama League and Drama Desk for Outstanding Lead Actor. ''Xanadu'' had several Tony Award nominations including "Best New Musical" for which Jackson and the cast performed on the 62nd Tony Awards show.

In 2008, Jackson joined Jane Krakowski and Sean Hayes in the New York City Center's Encores! production of ''Damn Yankees''. He returned to Encores! in 2009, playing Woody Mahoney in the staged concert of ''Finian's Rainbow'' which critics praised. Jackson also starred in the development workshop of ''Book of Mormon'' by Trey Parker, Matt Stone, and Robert Lopez, who co-wrote the music for ''Avenue Q''.

He has guest starred on television series including; ''Lipstick Jungle'', ''Life on Mars'', ''Ugly Betty'', and has a recurring role on the award winning NBC series, ''30 Rock''. On March 15, 2010, Jackson made his guest-starring debut on the long-running NBC series, ''Law & Order'' in an episode entitled ''Innocence''. Jackson filmed a sitcom pilot for ABC-TV called ''It Takes A Village'' co-starring Christopher Sieber and Leah Remini, which was not picked up for the fall 2010 season.

Jackson has starred in several notable webisode series including; "Cubby Bernstein" opposite Nathan Lane, "Legally Brown" with Allison Janney, and "The [title of show] Show" from the meta-fictional Broadway musical ''[Title of Show]''.

In March 2009, Jackson made his nightclub debut at Feinstein's at Lowes Regency with a sold out one man show titled "Back to the Start". He later teamed up with Michael Feinstein to create a well-received nightclub act titled "The Power of Two". A CD of the show was released on November 3, 2009.

In October 2009 Jackson opened on Broadway to positive critical reviews reprising the role of Woody Mahoney in the Broadway revival of the 1947 musical ''Finian's Rainbow'' at the St. James Theatre, costarring with Jim Norton and Kate Baldwin. ''The Wall Street Journal'' raved, "The way that [Kate Baldwin] and Cheyenne Jackson sing "Old Devil Moon" is the stuff best-selling cast albums are made of." The show closed on January 17, 2010.

Jackson was a featured performer on the ''New York Daily News'' float and telecast of NBC's coverage of the 83rd Annual Macy's Thanksgiving Day Parade singing "Play To Win", composed by Michael Feinstein and William Schermerhorn. Along with the company of ''Finian's Rainbow'', he recorded the Broadway revival cast album in early December 2009, with a release date of February 2, 2010.

Jackson is scheduled to be featured in a prominent guest role during Season 8 of ''Curb Your Enthusiasm''. His character "Terry" is the personal trainer to Larry David and Wanda Sykes.

Jackson was cast in ''Glee'' to play Dustin Goolsby, the coach of "Vocal Adrenaline," the main rival of "New Directions" for all of the show's second season.

''The Power of Two,'' a concert reuniting Jackson and Feinstein, was presented at Carnegie Hall on October 29, 2010. Jackson was the guest artist performing with the New York Pops in concert, "Cheyenne Jackson's Cocktail Hour: Music of the Mad Men Era," at Carnegie Hall on November 18, 2011. Joe Dziemianowicz of ''The New York Daily News'' wrote, "There, in Judy (Garland)'s spot singing Joni (Mitchell)’s song, (Cheyenne) Jackson turned the bittersweet ballad into a beautiful highlight in an evening filled with luscious moments with the New York Pops." In Spetember 2011, Cheyenne joined; Morgan Freeman, Ellen Barkin, Matt Bomer, Christine Lahti, and John Lithgow as part of the premier Broadway Cast of Dustin Lance Black’s new play “8″, directed by Joe Mantello.

Personal life

Jackson is openly gay and an LGBT rights supporter, as well as an ambassador for amfAR (The Foundation for AIDS Research) and the national ambassador for The Hetrick-Martin Institute. Jackson's husband, Monte Lapka, is a physicist; they have been together since 2000 and married on September 3, 2011 in New York.

Discography

Studio albums

{|class="wikitable" style="text-align:center;" |- ! rowspan="2"|Year ! rowspan="2"|Album details ! colspan="2"|Peak positions |- style="font-size:smaller;" ! style="width:30px;"| US Heat ! style="width:30px;"| US Jazz |- |2008 |align="left"|''The Power of Two'' (with Michael Feinstein)

Released: November 3, 2009

Label: Qualiton Imports, Harbinger Records

Formats: CD, digital download

| 17 || 15 |}

; Original Broadway Cast Albums

''Finian's Rainbow'' (2009)

''Xanadu'' (2007)

''All Shook Up'' (2005)

Professional credits

;Filmography

Year !! Title !! Role
rowspan="2"	2012	''Lola Versus''	Roger
''Mutual Friends''	Christoph
rowspan="3"	2011	''The Green''
''Price Check''	Ernie
''Smile''	Dr. Steve
2010 in film	2010	Photo Op (film)>Photo Op''
2008 in film	2008	''Hysteria''
2006 in film	2006	United 93 (film)>United 93''
2005 in film	2005	''Curiosity''

;Television

''Glee (TV series) ''It Takes a Village'' ''Law & Order'' ''30 Rock'' ''Life on Mars (U.S. TV series) ''Ugly Betty'' ''Lipstick Jungle (TV series) ''Family Practice''

Year !! Title !! Network!!Role
2011	''Curb Your Enthusiasm''	HBO
2010–2011	Glee'' ||	FOX	Dustin Goolsby (Coach of Vocal Adrenaline)
2010	|	ABC	Scott
2010	|	NBC	Guest Star
2009-Present	|	NBC	Danny (Jack) Baker
2009	Life on Mars''||	ABC	Guest Star, "Let All the Children Boogie"
2009	|	ABC	Guest Star, "Sugar Daddy"
2008	Lipstick Jungle''||	NBC	Guest Star, "Chapter Fifteen: The Sisterhood of the Traveling Prada"
2008	|	Lifetime	Series Lead

New York theater

''Finian's Rainbow'' ''Damn Yankees'' ''Xanadu (musical) ''The Agony and The Agony'' ''The 24 Hour Plays'' ''Altar Boyz'' ''Aida (musical) ''Thoroughly Modern Millie (play)

Year !! Title !! Role !! Notes
2010	''Finian's Rainbow''	Woody
2009	|	Woody	New York City Center ''Encores!''
2008	|	Joe Hardy	New York City Center ''Encores!''
2007	Xanadu'' ||	Sonny Malone (Original)	Helen Hayes Theatre
2006	|	Chet	Vineyard Theatre
rowspan="3"	2005	|	Kevin	American Airlines Theatre
''On the Twentieth Century''	"Life is Like a Train" Porter
''All Shook Up (musical)	All Shook Up''	Chad (Original)
2004	|	Matthew	Puerto Rican Traveling Theatre (NYMF production)
2003	Aida'' ||	Radames (Replacement)	Palace Theater
2002	Thoroughly Modern Millie'' ||	Jimmy Smith/ U/S Trevor Graydon (Replacement)	Marquis Theater

;Regional theater

''Hair (musical) ''West Side Story (musical) ''Joseph and the Amazing Technicolor Dreamcoat'' ''Beowulf'' ''Damn Yankees'' ''Carousel (musical) ''South Pacific (musical)

Year !! Title !! Role !! Company
	''The Rocky Horror Show''	Rocky
	Hair'' ||	Berger	5th Avenue Theatre, Seattle
	West Side Story'' ||	Tony	Village Theatre
	|	Joseph	Village Theatre
	|	Beowulf	Seattle Repertory Theatre
	|	Joe Hardy	Civic Light Opera
	Carousel'' ||	Billy	Civic Light Opera
	South Pacific'' ||	Lt. Cable	Carousel Players

Awards and honors

;Awards/honors: 2005 Theatre World Award, Outstanding Broadway Debut – ''All Shook Up'' 2006 Boston Society of Film Critics, Best Ensemble Cast – ''United 93'"

;Nominations: 2005 Outer Critics Circle Award, Outstanding Performance by a Lead Actor -''All Shook Up'' 2005 Drama League, Outstanding Performance by a Lead Actor – ''All Shook Up'' 2008 Drama Desk, Outstanding Performance by a Lead Actor – ''Xanadu'' 2008 Drama League, Distinguished Performance Award- ''Xanadu'' 2010 Drama Desk, Outstanding Performance by a Lead Actor – ''Finian's Rainbow''

References

External links

Cheyenne Jackson official Website

Interview on AfterElton.com

Category:Actors from Washington (state) Category:American film actors Category:American musical theatre actors Category:American stage actors Category:Gay actors Category:LGBT Native Americans Category:LGBT musicians from the United States Category:1975 births Category:Living people Category:American people of Native American descent

de:Cheyenne Jackson fa:شاین جکسون fr:Cheyenne Jackson it:Cheyenne Jackson ja:シャイアン・ジャクソン pl:Cheyenne Jackson pt:Cheyenne Jackson