(AP, top, and Ionis)

One day you’re a Southern California biotech company, doing whatever it is that Southern California biotech companies do. Discovering drugs, running clinical trials, filing patents, sending your scientists to meetings around the world.

The next day everyone and their neighbor recognizes your company’s name, and it’s not because of your groundbreaking RNA-targeting gene therapies.

That’s more or less what happened to the company formerly known as Isis Pharmaceuticals, a Carlsbad, Calif.-based drug developer, after the terror group (also known as the Islamic State) claimed that same name in 2013 and started wreaking global havoc.

On Friday, after more than a year of real or potential awkwardness, distraction and confusion, the company announced its new name, Ionis Pharmaceuticals.

What took them so long?

On one hand, a desire to not give in to the bad guys. “It’s our name. And I didn’t feel it was appropriate to respond to a terrorist organization in such a way. None of us did,” Stanley Crooke, the company’s chairman and CEO,told the Washington Post. On the other, the company’s mission is to treat diseases, not be named Isis. “We’re here for the patients. We’re not here for our name.”

So how exactly do you go from “Hey, that’s our name!” to “Fine, whatever, it’s all yours”?

There wasn’t one turning point, some clear trigger that the old name had to go. “It was the cumulative, sort of, intrusion into our lives that finally convinced us, ” he said.

Crooke, who founded his company in 1989, doesn’t remember the first time he heard about the terror group. “I’m aware of the world I live in, so I would have been aware of it probably the same time most Americans were.”

[Hello, my name is Isis — and I’m not a terrorist]

Over time, he said, “the comments, the questions, about our name and confusion about whether we were Isis Pharmaceuticals or some other Isis grew.”

Instead of people hearing about the company’s achievements, it was increasingly the name, the name, the name. In a private chat after an interview Friday, TV stock-picker Jim Cramer told Crooke that “when he would talk to people about the company, he would end up spending time trying to get them past the name,” Crooke said.

People kept asking not just will you change your name, but when? “That came from analysts. It came from investors. It came from people on the street — vendors, people who would visit, the neighbors of (employees). It was sort of a natural question.”

Then there was the risk of weirdness for doctors who were recruiting patients into clinical trials, if they needed to spend time explaining the company’s name instead of important medical details.

There may have even been confusion about the company’s identity at an airport. Crooke’s employees told him about the conversation they had with immigration and passport control, when they traveled to London for a conference:

“Why are you coming to England?“

“Well, I’m here for a scientific meeting.”

‘’Who do you work for?”

“Isis Pharmaceuticals.”

Agent raises eyebrows.

The terror attacks in Paris and San Bernardino contributed, too.

A few months ago, the company started talking internally about changing its name.

“I think what became apparent was that Isis is not going to go away in the near term, and it will be a news maker, and therefore that distractions are going to continue and continue to grow, probably for a while. I think that was the realization,” Crooke said.

Egyptian goddess Isis (iStock)

An early employee and former student of Crooke’s came up with the name Isis, inspired by the Egyptian goddess who was the patron of protection, magic and cures.

After many rounds of talks, employees came up with the new name without the help of outside consultants, and it cost under $200,000 to make the change, reported the San Diego Union-Tribune.

The new name, Ionis, sounds Greek, not Egyptian. And the new stock ticker is a scientist’s dream come true: IONS. In 2016, Ionis will finish three Phase 3 trials. One drug treats spinal muscular atrophy; another treats a disorder called TTR amyloidosis, which in one form leads to muscle and nerve failure and death; the third drug aims to treat until-now untreatable high-triglyceride diseases. “It’s an amazing, amazing year for us,” Crooke said.

Friday night, the company held a wake for its old name. People wore black armbands and talked about what Isis meant to them. There was snackfood and Irish Whiskey. Because it was a wake, after all.

Someone placed the company’s unofficial mascot, a three-foot-tall inflatable doll in the shape of Isis — the goddess, not the terror group — on a table, and people took pictures with her. And they told her goodbye.