The Bantams will be without their 12-goal hitman heading into tomorrow's game against Crewe.
But Shepherd believes that is part of the challenge as they aim to regain ground after a five-game winless run in the league.
The defender said: “If you look at his record you'll see he's scored a lot of goals, not just this season but throughout his time at Bradford.
“He will be missed big time but it is a chance for someone else to come in in the number 11 and fight for the shirt.
“We have a lot of players in the team and a lot of quality players who are not yet in the team, so it's up to someone to go out there and score goals and take the shirt for themselves.
“Everyone is chomping at the bit to get an opportunity, but it's really up to you. You can't argue anymore, it's what you do with it.”
Cook received his fifth caution of the season for the draw with Barrow and received a one-match suspension.
Shepherd has already been sent off, while Jamie Walker and Cheik Diabaté currently have one yellow card and are one game away from suspension. The cut-off point will be after 19 league games, which means Swindon will play at home next Saturday.
Neil Byrne will miss tomorrow's second game after being sent off against Morecambe in the FA Cup. Shepard has a lot of sympathy for his Baxley partner.
“We tried to contest, but personally, it's not a red card in my eyes. The referee gave it, but it was very, very soft.
“I made the appropriate decision and received a one-match suspension for five yellow cards. But I can't say too much about the referee.
“It's a contradiction. The rules aren't really set in stone. You can do one thing and get a reservation, the next week you can get a reservation, and the next week you can't get a reservation.
“It's like they're making up the rules and we can't do anything about it.”
Chris Long scored Crewe's winning goal against City last season (Image: @crewealexfc)
City recovered in midweek to pick up a point, but it was a flat outing that brought much criticism. They will have to face the fourth-placed Crew, who are undefeated in their last nine games.
Shepard admitted: “We were too lazy and sometimes too slow to really put any pressure on, but in the end we had good resilience and got the points.
“You can see we’re training well and now people are coming back and there’s a lot of competition for places.
“This is a team issue from 1 to 11 and something we need to look at and improve on.
“I think we can do it again, we have a lot of games so it will be over quickly.
“The good thing about football is that you can always get things right for the next game and that’s what we aim to do at Crewe.
“They're doing well at the moment, but every game in this league is tough. They're right up there so it's going to be a battle and we have to put on a good show.”