A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some biological benchmarking suites. We conclude with a comparison of our algorithm with some widely used motif discovery algorithms in the literature and suggest future directions for research in this area.

Laura Dexter letter, commenting on the McLeod murder trial, October 5, 1841

Alexander McLeod was Deputy Sheriff of the Niagara District during the Rebellion of 1837-38 in Upper Canada. On December 24, 1837, he became aware of a scheme by the rebels to use the American steamboat Caroline to provide supplies to William Lyon Mackenzie and his followers on Navy Island in the Niagara River. McLeod notified the authorities in Upper Canada about the situation. A few days later, on December 29, Commodore Andrew Drew led a band of men, including McLeod, to the American side, where the Caroline was moored at Schlosser’s Wharf. A scuffle ensued, in which American Amos Durfee was killed. The Caroline was then released from its moorings, set on fire, and drifted downstream before sinking. Many Americans viewed the incident as a violation of their sovereignty. Tensions between the United States and England were already strained over a boundary dispute between Maine and New Brunswick, and the situation with the Caroline further escalated the tension. McLeod was subsequently arrested in November, 1840 in Lewiston, NY and indicted for arson and murder. The British foreign secretary, Lord Palmerston, insisted that McLeod be released and could not be held personally responsible for the incident, as he was acting on orders from authorities in Canada. Eventually, McLeod was acquitted.

Photograph - Julia Cleveland Woodruff, Side angle Pose

Black and white photograph, mounted on board, 7 cm x 4 cm, of Julia in a side angle face pose. This photo was taken by Fred Pfaff of Peach Street, Erie, Pennsylvania.

Photograph - Margaret Julia Woodruff Band, Side Angle Lace Dress

Black and white photograph, 23 cm x 17 cm, of Margaret Julia Woodruff Band in a seated position, taken from a side angle. She is wearing a lace dress. The photo was taken by Dudley Hoyt of New York.

American Falls from Canadian side, Niagara, U.S.A.

The description reads "(12) American Falls from the Canadian side, Niagara, U.S.A."

Whirlpool and River View from Canadian side, Niagara

The description of the image reads "(18) Looking over the 'Whirlpool' and down the River - from Canadian side - Niagara, U.S.A."

Horseshoe Falls, Canada Side

The description of the image reads "29 Horseshoe Fall - Canada Side".

Cross sections of excavation required to make a ditch on the earth side of the railroad near Port Dalhousie

Cross sections of excavation required to make a ditch on the earth side of the railroad near Port Dalhousie. This is a 12 page booklet of hand- drawn charts and diagrams which is slightly stained. Text is not affected, Mar. 1860.

Envelope with a laurel wreath containing the initials W.N. on the back side

Envelope with a laurel wreath containing the initials W.N. on the back side. The envelope has a 2 cent stamp on it, but it is not addressed, n.d.

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5. This is signed by Fred Holmes, April 13, 1857.

Calculation of ditching in the south side of the feeder from Brown’s ditch culvert to lot no.5

Calculation of ditching in the south side of the feeder from Brown’s ditch culvert to lot no.5, n.d.

Cave of the Winds on the American Side Poster

Cave of the Winds on the American Side. This poster contains a poem by Mary S. Pond called Cave of the Winds, 35 cm. x 19 cm. The guides are listed as F.H. Johnson and Son. There is a portion of the poster missing from the upper left hand corner. This does affect the text. This newsprint article is mounted in a cardboard frame, 1860.

Some Incidents and Circumstances

- The first part of the document traces Mr. Haile’s lineage. His father, James Haile was a farmer. His grandfather, Amos Haile was a sailor for the early part of his life. He was placed on a British man-of- war in about 1758. He escaped and settled in Putney. (p.1) - His father’s mother’s maiden name was Parker. His mother’s maiden name was Campbell. Her father was a captain in the Revolutionary Army. (p.2) - His earliest memories revolve around the death of his aunt and the funeral of General Washington (although he did not witness this). At the time, his father was a Lieutenant in a regiment militia of Light Dragoons who wore red coats. (p.3) - In 1804, an addition was added to the Haile house which necessitated that William was to stay home to help with the building. He continued to study and read on his own. He was particularly interested in Napoleon Bonaparte’s victories. In that same year he was sent to Fairfield Academy where Reverend Caleb Alexander was the principal. (p.4) - On June 1, 1812, William was appointed as an Ensign in the Infantry of the Army of the United States. He was put into the recruiting service at Nassau (20 miles east of Albany) where he remained until September. (p.4) - He was assigned to the 11th Regiment of the W.S. Infantry and directed to proceed to Plattsburgh to report to Colonel Isaac Clark. (p.7) - He was assigned to the company commanded by Captain Samuel H. Halley who was not in the best of health and often absent. For a good part of the time William was in charge of the company. (p.8) - The 11th Regiment was encamped beside the 15th Regiment commanded by Col. Zebulon Montgomery Pike [Pike’s Peak was named after him]. Col. Pike generously drilled and disciplined the 11th Regiment since their officers didn’t seem capable of doing so. (p.8) - The first brigade to which William’s regiment was attached to was commanded by Brigadier General Bloomfield of New Jersey. Brigadier Chandler of Maine commanded the second brigade. (p.9) - At the beginning of November, Major General Dearborn took command of the army. He had been a good officer in his time, but William refers to him as “old and inefficient” earning him the nickname “Granny Dearborn” (p.9) - On November 17th, 1812, General Dearborn moved north with his army. The troops ended up in Champlain. There was no fighting, only a skirmish between a party of men under Colonel Pike and a few British troops who he succeeded in capturing. (p.10) - The troops were moved to barracks for the winter. Colonel Pike’s troops were put into suitable barracks and kept healthy but another part of the army (including the 11th Regiment) were sent to a barracks of green lumber north of Burlington. Disease soon broke out in the damp barracks and the hundreds of deaths soon followed. One morning, William counted 22 bodies who had died the previous night. He puts a lot of this down to an inexperienced commanding officer, General Chandler. (p.11) - At the beginning of 1813, William was stationed as a recruiter on the shore of Shoreham across from Fort Ticonderoga. In February, he returned to Burlington with his recruits. In March he received an order from General Chandler to proceed to Whitehall and take charge of the stores and provisions. In April and May it was decided that his half of the regiment (the First Battalion) should march to Sackett’s Harbour, Lake Ontario. They arrived at Sackett’s Harbour about the 10th of June, a few days after the Battle of Sackett’s Harbour. (p.12) - He was camped near the site of Fort Oswego and got word to head back to Sackett’s Harbour. A storm overtook the schooner that he was on. (p.14) - William was involved in the Battle of Williamsburg (or Chrysler’s Farm) which he calls a “stupid and bungling affair on the part of our generals”.(p. 18) - General Covington was wounded and died a few days after the battle. (p.19) - William speaks of being ill. The troops were ordered to march to Buffalo, but he is able to go to his father’s house in Fairfield where his mother nursed him back to health (p.23) - Upon arrival at Buffalo, the “old fogy Generals” were replaced with younger, more efficient men. (p.25) - On page 27 he sums up a few facts: In 1812, the army was assembled on Lake Champlain with the intention of capturing Montreal, and then Quebec. That year, under General Dearborn the army marched as far as Champlain, then turned back and went into winter quarters. In 1813, the army was assembled at Sackett’s Harbour and that year the campaign ended at French Mills which was 70 or 80 miles from Montreal. In 1814, the army at Buffalo were some 400 miles from Montreal with still the same object in view. - He says that these facts make “a riddle – difficult to explain”. (p.27) - On the evening of July 2nd they embarked on the boats with the objective of capturing Fort Erie. The enemy were all made prisoners of war (p.27) - On July 4th they went to Street’s Creek, 2 miles above the Chippewa [Chippawa] River (p.28) - Page 29 is titled The Battle of Chippewa [Chippawa] - He speaks of 2 drummers who were fighting over the possession of a drum when a cannonball came along and took of both of their heads (p.29) - He proclaims that this was one of the “most brilliant battles of the war”. The battle was fought and won in less than an hour after they left their tents. He credits General Scott with this success and states that was due to his rapid orders and movements. (p.30) - The dead of the battle remained on the field during the night. He describes this as quite gloomy seeing friend and foe lying side by side. At daybreak they set to work digging trenches to bury the dead. (p.31) - Colonel Campbell was wounded and advised to have his leg amputated. He refused, and subsequently died. (p.32) - It is said that the British threw several of their dead into the river and they went over the Falls. (p.32) - His troops repaired the bridge over Chippawa which the enemy had partially destroyed and then pursued the British as far as Queenston Heights. (p.32) - On pages 33 and 34 he speaks about meeting an old friend of his, Philip Harter. - The account ends at Queenston Heights