The Santa Clara County Medical Examiner-Coroner's Office late Tuesday afternoon confirmed her identity, which already was widely known in the community.
Holmes was the daughter of Thomas J. Holmes, a well-known aerospace engineer, and Natasha Holmes.
Her name was being withheld by school and counseling agency officials but was extensively published on Twitter and Facebook, two social-networking services. A link on Twitter points to an extensive posting of photos of Holmes at different ages.
Her parents are reportedly in isolation.
Her death has rocked Palo Alto emotionally, as it follows two earlier adolescent suicides on the train tracks, at least one suicide attempt by another teenager, and an earlier suicide of a 29-year-old Palo Alto woman.
In an effort to prevent future suicides, school, city, Caltrain and health care officials are joining forces with counselors in plans to put together a community-wide coalition. The coalition would design and implement an aggressive mental-health program targeted at adolescents and families.
Liz Kniss, president of the Santa Clara County Board of Supervisors, said the board's Health and Hospital Committee, which she chairs, will take up a proposed "Suicide Prevention Task Force" on which the council mental health staff has been working since June.
Kniss said she proposed the task force following the second adolescent death in early June. Nancy Pina, head of the county's Mental Health Department, has been working on it since.
On Monday, Caltrain officials echoed Kniss' call for a community-wide effort to address mental health issues.
Caltrain spokesman Mark Simon said at a news conference in San Carlos that the transit agency's employees are "devastated" by every death on the tracks. Caltrain is committed to preventing further deaths, Simon said, and is participating in the mental health task force in Palo Alto.
The agency conducts regular training for its transit security deputies and others to help them spot different types of mental illness, and defuse situations where people wish to harm themselves, according to Simon.
Caltrain considers awareness tactics more effective than reactive measures, such as surveillance cameras and extra police patrols, Simon said, adding that it is more realistic, and effective, to address the mental health issues behind these deaths than to focus on the tracks themselves.
"We have to find a way to encourage people not to step in front of our trains," he said. "You can't stop the train the way people would like us to."
Caltrain's service area, which includes San Francisco, San Mateo and Santa Clara counties, sees an average of 300 suicide deaths a year.